gmx_c_flags()
# This variable should be used for additional compiler flags which are not
-# generated in gmxCFlags nor are acceleration or MPI related.
+# generated in gmxCFlags nor are SIMD or MPI related.
set(EXTRA_C_FLAGS "")
+set(EXTRA_CXX_FLAGS "")
-# gcc 4.4.x is buggy and crashes when compiling some files with O3 and OpenMP on.
-# Detect here whether applying a workaround is needed and will apply it later
-# on the affected files.
-include(gmxGCC44O3BugWorkaround)
-gmx_check_gcc44_bug_workaround_needed(GMX_USE_GCC44_BUG_WORKAROUND)
-
-# clang 3.0 is buggy for some unknown reason detected during adding
-# the SSE2 group kernels for GROMACS 4.6. If we ever work out what
-# that is, we should replace these tests with a compiler feature test,
-# update GROMACS Redmine task #1039 and perhaps report a clang bug.
-#
-# In the meantime, until we require CMake 2.8.10 we cannot rely on it to detect
-# the compiler version for us. So we need a manual check for clang 3.0.
-include(gmxDetectClang30)
-gmx_detect_clang_3_0(COMPILER_IS_CLANG_3_0)
-if(COMPILER_IS_CLANG_3_0)
- message(FATAL_ERROR "Your compiler is clang version 3.0, which is known to be buggy for GROMACS. Use a different compiler.")
-endif()
-
-# clang <=3.2 contains a bug that causes incorrect code to be generated for the
-# vfmaddps instruction and therefore the bug is triggered with AVX_128_FMA.
-# (see: http://llvm.org/bugs/show_bug.cgi?id=15040).
-# We can work around this by not using the integrated assembler (except on OS X
-# which has an outdated assembler that does not support AVX instructions).
-if (${CMAKE_C_COMPILER_ID} MATCHES "Clang" AND C_COMPILER_VERSION VERSION_LESS "3.3")
- set(GMX_USE_CLANG_FMA_BUG_WORKAROUND TRUE)
-endif()
-
-# GMX_CPU_ACCELERATION will not be set automatically until the second
+# Run through a number of tests for buggy compilers and other issues
+include(gmxTestCompilerProblems)
+gmx_test_compiler_problems()
++# GMX_SIMD will not be set automatically until the second
+ # pass (which is not strictly guaranteed to occur), so putting this
+ # check here among logically-related tests is inefficient, but the
+ # potential loss is likely zero.
-if(GMX_CPU_ACCELERATION STREQUAL "AVX_256"
++if(GMX_SIMD STREQUAL "AVX_256"
+ AND CMAKE_COMPILER_IS_GNUCC
+ AND (C_COMPILER_VERSION VERSION_EQUAL "4.6.1"
+ OR CXX_COMPILER_VERSION VERSION_EQUAL "4.6.1"))
- message(FATAL_ERROR "gcc 4.6.1 has buggy support for AVX, and GROMACS mdrun will not work. If you want simulation performance, use a more recent compiler. Otherwise, use GMX_CPU_ACCELERATION=SSE4.1")
++ message(FATAL_ERROR "gcc 4.6.1 has buggy support for AVX, and GROMACS mdrun will not work. If you want simulation performance, use a more recent compiler. Otherwise, use GMX_SIMD=SSE4.1")
+ # See http://gcc.gnu.org/bugzilla/show_bug.cgi?id=49002
+ endif()
+
-if (CMAKE_C_COMPILER_ID STREQUAL "PGI")
- message(WARNING "All tested PGI compiler versions (up to 12.9.0) generate binaries which produce incorrect results, or even fail to compile Gromacs. Highly recommended to use a different compiler. If you choose to use PGI, make sure to run the regressiontests.")
-endif()
-if(CMAKE_C_COMPILER_ID MATCHES "Intel" AND C_COMPILER_VERSION VERSION_LESS "12.0.0")
- message(WARNING "Intel compilers before 12.0.0 are not routinely tested, so there may be problems. Version 11.1 with SSE4.1 is known to produce incorrect results. It is highly recommended to use a more up-to-date compiler. If you choose to use this version, make sure you run the regressiontests.")
-endif()
set(PKG_CFLAGS "")
if(GMX_DOUBLE)
--- /dev/null
- for (i = 0; (i < ndim); i++)
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
+ * Copyright (c) 2001-2004, The GROMACS development team.
+ * Copyright (c) 2013,2014, by the GROMACS development team, led by
+ * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+ * and including many others, as listed in the AUTHORS file in the
+ * top-level source directory and at http://www.gromacs.org.
+ *
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
+ * of the License, or (at your option) any later version.
+ *
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+ *
+ * If you want to redistribute modifications to GROMACS, please
+ * consider that scientific software is very special. Version
+ * control is crucial - bugs must be traceable. We will be happy to
+ * consider code for inclusion in the official distribution, but
+ * derived work must not be called official GROMACS. Details are found
+ * in the README & COPYING files - if they are missing, get the
+ * official version at http://www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the research papers on the package. Check out http://www.gromacs.org.
+ */
+#ifdef HAVE_CONFIG_H
+#include <config.h>
+#endif
+
+#include <math.h>
+#include <string.h>
+#include <time.h>
+
+#ifdef HAVE_SYS_TIME_H
+#include <sys/time.h>
+#endif
+
+#include "gromacs/commandline/pargs.h"
+#include "sysstuff.h"
+#include "typedefs.h"
+#include "gromacs/utility/smalloc.h"
+#include "macros.h"
+#include "vec.h"
+#include "pbc.h"
+#include "gromacs/fileio/futil.h"
+#include "index.h"
+#include "gromacs/fileio/confio.h"
+#include "gromacs/fileio/trnio.h"
+#include "mshift.h"
+#include "xvgr.h"
+#include "rmpbc.h"
+#include "txtdump.h"
+#include "gromacs/fileio/matio.h"
+#include "eigio.h"
+#include "physics.h"
+#include "gmx_ana.h"
+#include "gromacs/utility/cstringutil.h"
+#include "gromacs/fileio/trxio.h"
+
+#include "gromacs/linearalgebra/eigensolver.h"
+#include "gromacs/math/do_fit.h"
+#include "gromacs/legacyheaders/gmx_fatal.h"
+
+int gmx_covar(int argc, char *argv[])
+{
+ const char *desc[] = {
+ "[THISMODULE] calculates and diagonalizes the (mass-weighted)",
+ "covariance matrix.",
+ "All structures are fitted to the structure in the structure file.",
+ "When this is not a run input file periodicity will not be taken into",
+ "account. When the fit and analysis groups are identical and the analysis",
+ "is non mass-weighted, the fit will also be non mass-weighted.",
+ "[PAR]",
+ "The eigenvectors are written to a trajectory file ([TT]-v[tt]).",
+ "When the same atoms are used for the fit and the covariance analysis,",
+ "the reference structure for the fit is written first with t=-1.",
+ "The average (or reference when [TT]-ref[tt] is used) structure is",
+ "written with t=0, the eigenvectors",
+ "are written as frames with the eigenvector number as timestamp.",
+ "[PAR]",
+ "The eigenvectors can be analyzed with [gmx-anaeig].",
+ "[PAR]",
+ "Option [TT]-ascii[tt] writes the whole covariance matrix to",
+ "an ASCII file. The order of the elements is: x1x1, x1y1, x1z1, x1x2, ...",
+ "[PAR]",
+ "Option [TT]-xpm[tt] writes the whole covariance matrix to an [TT].xpm[tt] file.",
+ "[PAR]",
+ "Option [TT]-xpma[tt] writes the atomic covariance matrix to an [TT].xpm[tt] file,",
+ "i.e. for each atom pair the sum of the xx, yy and zz covariances is",
+ "written.",
+ "[PAR]",
+ "Note that the diagonalization of a matrix requires memory and time",
+ "that will increase at least as fast as than the square of the number",
+ "of atoms involved. It is easy to run out of memory, in which",
+ "case this tool will probably exit with a 'Segmentation fault'. You",
+ "should consider carefully whether a reduced set of atoms will meet",
+ "your needs for lower costs."
+ };
+ static gmx_bool bFit = TRUE, bRef = FALSE, bM = FALSE, bPBC = TRUE;
+ static int end = -1;
+ t_pargs pa[] = {
+ { "-fit", FALSE, etBOOL, {&bFit},
+ "Fit to a reference structure"},
+ { "-ref", FALSE, etBOOL, {&bRef},
+ "Use the deviation from the conformation in the structure file instead of from the average" },
+ { "-mwa", FALSE, etBOOL, {&bM},
+ "Mass-weighted covariance analysis"},
+ { "-last", FALSE, etINT, {&end},
+ "Last eigenvector to write away (-1 is till the last)" },
+ { "-pbc", FALSE, etBOOL, {&bPBC},
+ "Apply corrections for periodic boundary conditions" }
+ };
+ FILE *out;
+ t_trxstatus *status;
+ t_trxstatus *trjout;
+ t_topology top;
+ int ePBC;
+ t_atoms *atoms;
+ rvec *x, *xread, *xref, *xav, *xproj;
+ matrix box, zerobox;
+ real *sqrtm, *mat, *eigenvalues, sum, trace, inv_nframes;
+ real t, tstart, tend, **mat2;
+ real xj, *w_rls = NULL;
+ real min, max, *axis;
+ int ntopatoms, step;
+ int natoms, nat, count, nframes0, nframes, nlevels;
+ gmx_int64_t ndim, i, j, k, l;
+ int WriteXref;
+ const char *fitfile, *trxfile, *ndxfile;
+ const char *eigvalfile, *eigvecfile, *averfile, *logfile;
+ const char *asciifile, *xpmfile, *xpmafile;
+ char str[STRLEN], *fitname, *ananame, *pcwd;
+ int d, dj, nfit;
+ atom_id *index, *ifit;
+ gmx_bool bDiffMass1, bDiffMass2;
+ time_t now;
+ char timebuf[STRLEN];
+ t_rgb rlo, rmi, rhi;
+ real *eigenvectors;
+ output_env_t oenv;
+ gmx_rmpbc_t gpbc = NULL;
+
+ t_filenm fnm[] = {
+ { efTRX, "-f", NULL, ffREAD },
+ { efTPS, NULL, NULL, ffREAD },
+ { efNDX, NULL, NULL, ffOPTRD },
+ { efXVG, NULL, "eigenval", ffWRITE },
+ { efTRN, "-v", "eigenvec", ffWRITE },
+ { efSTO, "-av", "average.pdb", ffWRITE },
+ { efLOG, NULL, "covar", ffWRITE },
+ { efDAT, "-ascii", "covar", ffOPTWR },
+ { efXPM, "-xpm", "covar", ffOPTWR },
+ { efXPM, "-xpma", "covara", ffOPTWR }
+ };
+#define NFILE asize(fnm)
+
+ if (!parse_common_args(&argc, argv, PCA_CAN_TIME | PCA_TIME_UNIT | PCA_BE_NICE,
+ NFILE, fnm, asize(pa), pa, asize(desc), desc, 0, NULL, &oenv))
+ {
+ return 0;
+ }
+
+ clear_mat(zerobox);
+
+ fitfile = ftp2fn(efTPS, NFILE, fnm);
+ trxfile = ftp2fn(efTRX, NFILE, fnm);
+ ndxfile = ftp2fn_null(efNDX, NFILE, fnm);
+ eigvalfile = ftp2fn(efXVG, NFILE, fnm);
+ eigvecfile = ftp2fn(efTRN, NFILE, fnm);
+ averfile = ftp2fn(efSTO, NFILE, fnm);
+ logfile = ftp2fn(efLOG, NFILE, fnm);
+ asciifile = opt2fn_null("-ascii", NFILE, fnm);
+ xpmfile = opt2fn_null("-xpm", NFILE, fnm);
+ xpmafile = opt2fn_null("-xpma", NFILE, fnm);
+
+ read_tps_conf(fitfile, str, &top, &ePBC, &xref, NULL, box, TRUE);
+ atoms = &top.atoms;
+
+ if (bFit)
+ {
+ printf("\nChoose a group for the least squares fit\n");
+ get_index(atoms, ndxfile, 1, &nfit, &ifit, &fitname);
+ if (nfit < 3)
+ {
+ gmx_fatal(FARGS, "Need >= 3 points to fit!\n");
+ }
+ }
+ else
+ {
+ nfit = 0;
+ }
+ printf("\nChoose a group for the covariance analysis\n");
+ get_index(atoms, ndxfile, 1, &natoms, &index, &ananame);
+
+ bDiffMass1 = FALSE;
+ if (bFit)
+ {
+ snew(w_rls, atoms->nr);
+ for (i = 0; (i < nfit); i++)
+ {
+ w_rls[ifit[i]] = atoms->atom[ifit[i]].m;
+ if (i)
+ {
+ bDiffMass1 = bDiffMass1 || (w_rls[ifit[i]] != w_rls[ifit[i-1]]);
+ }
+ }
+ }
+ bDiffMass2 = FALSE;
+ snew(sqrtm, natoms);
+ for (i = 0; (i < natoms); i++)
+ {
+ if (bM)
+ {
+ sqrtm[i] = sqrt(atoms->atom[index[i]].m);
+ if (i)
+ {
+ bDiffMass2 = bDiffMass2 || (sqrtm[i] != sqrtm[i-1]);
+ }
+ }
+ else
+ {
+ sqrtm[i] = 1.0;
+ }
+ }
+
+ if (bFit && bDiffMass1 && !bDiffMass2)
+ {
+ bDiffMass1 = natoms != nfit;
+ i = 0;
+ for (i = 0; (i < natoms) && !bDiffMass1; i++)
+ {
+ bDiffMass1 = index[i] != ifit[i];
+ }
+ if (!bDiffMass1)
+ {
+ fprintf(stderr, "\n"
+ "Note: the fit and analysis group are identical,\n"
+ " while the fit is mass weighted and the analysis is not.\n"
+ " Making the fit non mass weighted.\n\n");
+ for (i = 0; (i < nfit); i++)
+ {
+ w_rls[ifit[i]] = 1.0;
+ }
+ }
+ }
+
+ /* Prepare reference frame */
+ if (bPBC)
+ {
+ gpbc = gmx_rmpbc_init(&top.idef, ePBC, atoms->nr);
+ gmx_rmpbc(gpbc, atoms->nr, box, xref);
+ }
+ if (bFit)
+ {
+ reset_x(nfit, ifit, atoms->nr, NULL, xref, w_rls);
+ }
+
+ snew(x, natoms);
+ snew(xav, natoms);
+ ndim = natoms*DIM;
+ if (sqrt(GMX_INT64_MAX) < ndim)
+ {
+ gmx_fatal(FARGS, "Number of degrees of freedoms to large for matrix.\n");
+ }
+ snew(mat, ndim*ndim);
+
+ fprintf(stderr, "Calculating the average structure ...\n");
+ nframes0 = 0;
+ nat = read_first_x(oenv, &status, trxfile, &t, &xread, box);
+ if (nat != atoms->nr)
+ {
+ fprintf(stderr, "\nWARNING: number of atoms in tpx (%d) and trajectory (%d) do not match\n", natoms, nat);
+ }
+ do
+ {
+ nframes0++;
+ /* calculate x: a fitted struture of the selected atoms */
+ if (bPBC)
+ {
+ gmx_rmpbc(gpbc, nat, box, xread);
+ }
+ if (bFit)
+ {
+ reset_x(nfit, ifit, nat, NULL, xread, w_rls);
+ do_fit(nat, w_rls, xref, xread);
+ }
+ for (i = 0; i < natoms; i++)
+ {
+ rvec_inc(xav[i], xread[index[i]]);
+ }
+ }
+ while (read_next_x(oenv, status, &t, xread, box));
+ close_trj(status);
+
+ inv_nframes = 1.0/nframes0;
+ for (i = 0; i < natoms; i++)
+ {
+ for (d = 0; d < DIM; d++)
+ {
+ xav[i][d] *= inv_nframes;
+ xread[index[i]][d] = xav[i][d];
+ }
+ }
+ write_sto_conf_indexed(opt2fn("-av", NFILE, fnm), "Average structure",
+ atoms, xread, NULL, epbcNONE, zerobox, natoms, index);
+ sfree(xread);
+
+ fprintf(stderr, "Constructing covariance matrix (%dx%d) ...\n", (int)ndim, (int)ndim);
+ nframes = 0;
+ nat = read_first_x(oenv, &status, trxfile, &t, &xread, box);
+ tstart = t;
+ do
+ {
+ nframes++;
+ tend = t;
+ /* calculate x: a (fitted) structure of the selected atoms */
+ if (bPBC)
+ {
+ gmx_rmpbc(gpbc, nat, box, xread);
+ }
+ if (bFit)
+ {
+ reset_x(nfit, ifit, nat, NULL, xread, w_rls);
+ do_fit(nat, w_rls, xref, xread);
+ }
+ if (bRef)
+ {
+ for (i = 0; i < natoms; i++)
+ {
+ rvec_sub(xread[index[i]], xref[index[i]], x[i]);
+ }
+ }
+ else
+ {
+ for (i = 0; i < natoms; i++)
+ {
+ rvec_sub(xread[index[i]], xav[i], x[i]);
+ }
+ }
+
+ for (j = 0; j < natoms; j++)
+ {
+ for (dj = 0; dj < DIM; dj++)
+ {
+ k = ndim*(DIM*j+dj);
+ xj = x[j][dj];
+ for (i = j; i < natoms; i++)
+ {
+ l = k+DIM*i;
+ for (d = 0; d < DIM; d++)
+ {
+ mat[l+d] += x[i][d]*xj;
+ }
+ }
+ }
+ }
+ }
+ while (read_next_x(oenv, status, &t, xread, box) &&
+ (bRef || nframes < nframes0));
+ close_trj(status);
+ gmx_rmpbc_done(gpbc);
+
+ fprintf(stderr, "Read %d frames\n", nframes);
+
+ if (bRef)
+ {
+ /* copy the reference structure to the ouput array x */
+ snew(xproj, natoms);
+ for (i = 0; i < natoms; i++)
+ {
+ copy_rvec(xref[index[i]], xproj[i]);
+ }
+ }
+ else
+ {
+ xproj = xav;
+ }
+
+ /* correct the covariance matrix for the mass */
+ inv_nframes = 1.0/nframes;
+ for (j = 0; j < natoms; j++)
+ {
+ for (dj = 0; dj < DIM; dj++)
+ {
+ for (i = j; i < natoms; i++)
+ {
+ k = ndim*(DIM*j+dj)+DIM*i;
+ for (d = 0; d < DIM; d++)
+ {
+ mat[k+d] = mat[k+d]*inv_nframes*sqrtm[i]*sqrtm[j];
+ }
+ }
+ }
+ }
+
+ /* symmetrize the matrix */
+ for (j = 0; j < ndim; j++)
+ {
+ for (i = j; i < ndim; i++)
+ {
+ mat[ndim*i+j] = mat[ndim*j+i];
+ }
+ }
+
+ trace = 0;
+ for (i = 0; i < ndim; i++)
+ {
+ trace += mat[i*ndim+i];
+ }
+ fprintf(stderr, "\nTrace of the covariance matrix: %g (%snm^2)\n",
+ trace, bM ? "u " : "");
+
+ if (asciifile)
+ {
+ out = gmx_ffopen(asciifile, "w");
+ for (j = 0; j < ndim; j++)
+ {
+ for (i = 0; i < ndim; i += 3)
+ {
+ fprintf(out, "%g %g %g\n",
+ mat[ndim*j+i], mat[ndim*j+i+1], mat[ndim*j+i+2]);
+ }
+ }
+ gmx_ffclose(out);
+ }
+
+ if (xpmfile)
+ {
+ min = 0;
+ max = 0;
+ snew(mat2, ndim);
+ for (j = 0; j < ndim; j++)
+ {
+ mat2[j] = &(mat[ndim*j]);
+ for (i = 0; i <= j; i++)
+ {
+ if (mat2[j][i] < min)
+ {
+ min = mat2[j][i];
+ }
+ if (mat2[j][j] > max)
+ {
+ max = mat2[j][i];
+ }
+ }
+ }
+ snew(axis, ndim);
+ for (i = 0; i < ndim; i++)
+ {
+ axis[i] = i+1;
+ }
+ rlo.r = 0; rlo.g = 0; rlo.b = 1;
+ rmi.r = 1; rmi.g = 1; rmi.b = 1;
+ rhi.r = 1; rhi.g = 0; rhi.b = 0;
+ out = gmx_ffopen(xpmfile, "w");
+ nlevels = 80;
+ write_xpm3(out, 0, "Covariance", bM ? "u nm^2" : "nm^2",
+ "dim", "dim", ndim, ndim, axis, axis,
+ mat2, min, 0.0, max, rlo, rmi, rhi, &nlevels);
+ gmx_ffclose(out);
+ sfree(axis);
+ sfree(mat2);
+ }
+
+ if (xpmafile)
+ {
+ min = 0;
+ max = 0;
+ snew(mat2, ndim/DIM);
+ for (i = 0; i < ndim/DIM; i++)
+ {
+ snew(mat2[i], ndim/DIM);
+ }
+ for (j = 0; j < ndim/DIM; j++)
+ {
+ for (i = 0; i <= j; i++)
+ {
+ mat2[j][i] = 0;
+ for (d = 0; d < DIM; d++)
+ {
+ mat2[j][i] += mat[ndim*(DIM*j+d)+DIM*i+d];
+ }
+ if (mat2[j][i] < min)
+ {
+ min = mat2[j][i];
+ }
+ if (mat2[j][j] > max)
+ {
+ max = mat2[j][i];
+ }
+ mat2[i][j] = mat2[j][i];
+ }
+ }
+ snew(axis, ndim/DIM);
+ for (i = 0; i < ndim/DIM; i++)
+ {
+ axis[i] = i+1;
+ }
+ rlo.r = 0; rlo.g = 0; rlo.b = 1;
+ rmi.r = 1; rmi.g = 1; rmi.b = 1;
+ rhi.r = 1; rhi.g = 0; rhi.b = 0;
+ out = gmx_ffopen(xpmafile, "w");
+ nlevels = 80;
+ write_xpm3(out, 0, "Covariance", bM ? "u nm^2" : "nm^2",
+ "atom", "atom", ndim/DIM, ndim/DIM, axis, axis,
+ mat2, min, 0.0, max, rlo, rmi, rhi, &nlevels);
+ gmx_ffclose(out);
+ sfree(axis);
+ for (i = 0; i < ndim/DIM; i++)
+ {
+ sfree(mat2[i]);
+ }
+ sfree(mat2);
+ }
+
+
+ /* call diagonalization routine */
+
+ snew(eigenvalues, ndim);
+ snew(eigenvectors, ndim*ndim);
+
+ memcpy(eigenvectors, mat, ndim*ndim*sizeof(real));
+ fprintf(stderr, "\nDiagonalizing ...\n");
+ fflush(stderr);
+ eigensolver(eigenvectors, ndim, 0, ndim, eigenvalues, mat);
+ sfree(eigenvectors);
+
+ /* now write the output */
+
+ sum = 0;
+ for (i = 0; i < ndim; i++)
+ {
+ sum += eigenvalues[i];
+ }
+ fprintf(stderr, "\nSum of the eigenvalues: %g (%snm^2)\n",
+ sum, bM ? "u " : "");
+ if (fabs(trace-sum) > 0.01*trace)
+ {
+ fprintf(stderr, "\nWARNING: eigenvalue sum deviates from the trace of the covariance matrix\n");
+ }
+
+ fprintf(stderr, "\nWriting eigenvalues to %s\n", eigvalfile);
+
+ sprintf(str, "(%snm\\S2\\N)", bM ? "u " : "");
+ out = xvgropen(eigvalfile,
+ "Eigenvalues of the covariance matrix",
+ "Eigenvector index", str, oenv);
- fprintf(out, "Wrote %d eigenvalues to %s\n", (int)ndim, eigvalfile);
++ for (i = 0; (i < end); i++)
+ {
+ fprintf (out, "%10d %g\n", (int)i+1, eigenvalues[ndim-1-i]);
+ }
+ gmx_ffclose(out);
+
+ if (end == -1)
+ {
+ if (nframes-1 < ndim)
+ {
+ end = nframes-1;
++ fprintf(out, "WARNING: there are fewer frames in your trajectory than there are\n");
++ fprintf(out, "degrees of freedom in your system. Only generating the first\n");
++ fprintf(out, "%d out of %d eigenvectors and eigenvalues.\n", end, (int)ndim);
+ }
+ else
+ {
+ end = ndim;
+ }
+ }
+ if (bFit)
+ {
+ /* misuse lambda: 0/1 mass weighted analysis no/yes */
+ if (nfit == natoms)
+ {
+ WriteXref = eWXR_YES;
+ for (i = 0; i < nfit; i++)
+ {
+ copy_rvec(xref[ifit[i]], x[i]);
+ }
+ }
+ else
+ {
+ WriteXref = eWXR_NO;
+ }
+ }
+ else
+ {
+ /* misuse lambda: -1 for no fit */
+ WriteXref = eWXR_NOFIT;
+ }
+
+ write_eigenvectors(eigvecfile, natoms, mat, TRUE, 1, end,
+ WriteXref, x, bDiffMass1, xproj, bM, eigenvalues);
+
+ out = gmx_ffopen(logfile, "w");
+
+ time(&now);
+ gmx_ctime_r(&now, timebuf, STRLEN);
+ fprintf(out, "Covariance analysis log, written %s\n", timebuf);
+
+ fprintf(out, "Program: %s\n", argv[0]);
+ gmx_getcwd(str, STRLEN);
+
+ fprintf(out, "Working directory: %s\n\n", str);
+
+ fprintf(out, "Read %d frames from %s (time %g to %g %s)\n", nframes, trxfile,
+ output_env_conv_time(oenv, tstart), output_env_conv_time(oenv, tend), output_env_get_time_unit(oenv));
+ if (bFit)
+ {
+ fprintf(out, "Read reference structure for fit from %s\n", fitfile);
+ }
+ if (ndxfile)
+ {
+ fprintf(out, "Read index groups from %s\n", ndxfile);
+ }
+ fprintf(out, "\n");
+
+ fprintf(out, "Analysis group is '%s' (%d atoms)\n", ananame, natoms);
+ if (bFit)
+ {
+ fprintf(out, "Fit group is '%s' (%d atoms)\n", fitname, nfit);
+ }
+ else
+ {
+ fprintf(out, "No fit was used\n");
+ }
+ fprintf(out, "Analysis is %smass weighted\n", bDiffMass2 ? "" : "non-");
+ if (bFit)
+ {
+ fprintf(out, "Fit is %smass weighted\n", bDiffMass1 ? "" : "non-");
+ }
+ fprintf(out, "Diagonalized the %dx%d covariance matrix\n", (int)ndim, (int)ndim);
+ fprintf(out, "Trace of the covariance matrix before diagonalizing: %g\n",
+ trace);
+ fprintf(out, "Trace of the covariance matrix after diagonalizing: %g\n\n",
+ sum);
+
++ fprintf(out, "Wrote %d eigenvalues to %s\n", (int)end, eigvalfile);
+ if (WriteXref == eWXR_YES)
+ {
+ fprintf(out, "Wrote reference structure to %s\n", eigvecfile);
+ }
+ fprintf(out, "Wrote average structure to %s and %s\n", averfile, eigvecfile);
+ fprintf(out, "Wrote eigenvectors %d to %d to %s\n", 1, end, eigvecfile);
+
+ gmx_ffclose(out);
+
+ fprintf(stderr, "Wrote the log to %s\n", logfile);
+
+ return 0;
+}
--- /dev/null
- "from. One needs an energy file with the following components:",
- "Coul (A-B) LJ-SR (A-B) etc."
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
+ * Copyright (c) 2001-2004, The GROMACS development team.
+ * Copyright (c) 2013,2014, by the GROMACS development team, led by
+ * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+ * and including many others, as listed in the AUTHORS file in the
+ * top-level source directory and at http://www.gromacs.org.
+ *
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
+ * of the License, or (at your option) any later version.
+ *
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+ *
+ * If you want to redistribute modifications to GROMACS, please
+ * consider that scientific software is very special. Version
+ * control is crucial - bugs must be traceable. We will be happy to
+ * consider code for inclusion in the official distribution, but
+ * derived work must not be called official GROMACS. Details are found
+ * in the README & COPYING files - if they are missing, get the
+ * official version at http://www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the research papers on the package. Check out http://www.gromacs.org.
+ */
+#ifdef HAVE_CONFIG_H
+#include <config.h>
+#endif
+
+#include <stdio.h>
+#include <stdlib.h>
+#include <math.h>
+#include <string.h>
+
+#include "gromacs/commandline/pargs.h"
+#include "sysstuff.h"
+#include "typedefs.h"
+#include "gromacs/utility/smalloc.h"
+#include "macros.h"
+#include "vec.h"
+#include "gromacs/fileio/futil.h"
+#include "txtdump.h"
+#include "gromacs/fileio/enxio.h"
+#include "gstat.h"
+#include "xvgr.h"
+#include "gmx_ana.h"
+#include "gromacs/fileio/trxio.h"
+
+typedef struct {
+ int nlj, nqq;
+ int *lj;
+ int *qq;
+} t_liedata;
+
+static t_liedata *analyze_names(int nre, gmx_enxnm_t *names, const char *ligand)
+{
+ int i;
+ t_liedata *ld;
+ char self[256];
+
+ /* Skip until we come to pressure */
+ for (i = 0; (i < F_NRE); i++)
+ {
+ if (strcmp(names[i].name, interaction_function[F_PRES].longname) == 0)
+ {
+ break;
+ }
+ }
+
+ /* Now real analysis: find components of energies */
+ sprintf(self, "%s-%s", ligand, ligand);
+ snew(ld, 1);
+ for (; (i < nre); i++)
+ {
+ if ((strstr(names[i].name, ligand) != NULL) &&
+ (strstr(names[i].name, self) == NULL))
+ {
+ if (strstr(names[i].name, "LJ") != NULL)
+ {
+ ld->nlj++;
+ srenew(ld->lj, ld->nlj);
+ ld->lj[ld->nlj-1] = i;
+ }
+ else if (strstr(names[i].name, "Coul") != NULL)
+ {
+ ld->nqq++;
+ srenew(ld->qq, ld->nqq);
+ ld->qq[ld->nqq-1] = i;
+ }
+ }
+ }
+ printf("Using the following energy terms:\n");
+ printf("LJ: ");
+ for (i = 0; (i < ld->nlj); i++)
+ {
+ printf(" %12s", names[ld->lj[i]].name);
+ }
+ printf("\nCoul:");
+ for (i = 0; (i < ld->nqq); i++)
+ {
+ printf(" %12s", names[ld->qq[i]].name);
+ }
+ printf("\n");
+
+ return ld;
+}
+
+real calc_lie(t_liedata *ld, t_energy ee[], real lie_lj, real lie_qq,
+ real fac_lj, real fac_qq)
+{
+ int i;
+ real lj_tot, qq_tot;
+
+ lj_tot = 0;
+ for (i = 0; (i < ld->nlj); i++)
+ {
+ lj_tot += ee[ld->lj[i]].e;
+ }
+ qq_tot = 0;
+ for (i = 0; (i < ld->nqq); i++)
+ {
+ qq_tot += ee[ld->qq[i]].e;
+ }
+
+ /* And now the great LIE formula: */
+ return fac_lj*(lj_tot-lie_lj)+fac_qq*(qq_tot-lie_qq);
+}
+
+int gmx_lie(int argc, char *argv[])
+{
+ const char *desc[] = {
+ "[THISMODULE] computes a free energy estimate based on an energy analysis",
++ "from nonbonded energies. One needs an energy file with the following components:",
++ "Coul-(A-B) LJ-SR (A-B) etc.[PAR]",
++ "To utilize [TT]g_lie[tt] correctly, two simulations are required: one with the",
++ "molecule of interest bound to its receptor and one with the molecule in water.",
++ "Both need to utilize [TT]energygrps[tt] such that Coul-SR(A-B), LJ-SR(A-B), etc. terms",
++ "are written to the [TT].edr[tt] file. Values from the molecule-in-water simulation",
++ "are necessary for supplying suitable values for -Elj and -Eqq."
+ };
+ static real lie_lj = 0, lie_qq = 0, fac_lj = 0.181, fac_qq = 0.5;
+ static const char *ligand = "none";
+ t_pargs pa[] = {
+ { "-Elj", FALSE, etREAL, {&lie_lj},
+ "Lennard-Jones interaction between ligand and solvent" },
+ { "-Eqq", FALSE, etREAL, {&lie_qq},
+ "Coulomb interaction between ligand and solvent" },
+ { "-Clj", FALSE, etREAL, {&fac_lj},
+ "Factor in the LIE equation for Lennard-Jones component of energy" },
+ { "-Cqq", FALSE, etREAL, {&fac_qq},
+ "Factor in the LIE equation for Coulomb component of energy" },
+ { "-ligand", FALSE, etSTR, {&ligand},
+ "Name of the ligand in the energy file" }
+ };
+#define NPA asize(pa)
+
+ FILE *out;
+ int nre, nframes = 0, ct = 0;
+ ener_file_t fp;
+ gmx_bool bCont;
+ t_liedata *ld;
+ gmx_enxnm_t *enm = NULL;
+ t_enxframe *fr;
+ real lie;
+ double lieaver = 0, lieav2 = 0;
+ output_env_t oenv;
+
+ t_filenm fnm[] = {
+ { efEDR, "-f", "ener", ffREAD },
+ { efXVG, "-o", "lie", ffWRITE }
+ };
+#define NFILE asize(fnm)
+
+ if (!parse_common_args(&argc, argv, PCA_CAN_VIEW | PCA_CAN_TIME | PCA_BE_NICE,
+ NFILE, fnm, NPA, pa, asize(desc), desc, 0, NULL, &oenv))
+ {
+ return 0;
+ }
+
+ fp = open_enx(ftp2fn(efEDR, NFILE, fnm), "r");
+ do_enxnms(fp, &nre, &enm);
+
+ ld = analyze_names(nre, enm, ligand);
+ snew(fr, 1);
++
+ out = xvgropen(ftp2fn(efXVG, NFILE, fnm), "LIE free energy estimate",
+ "Time (ps)", "DGbind (kJ/mol)", oenv);
+ while (do_enx(fp, fr))
+ {
+ ct = check_times(fr->t);
+ if (ct == 0)
+ {
+ lie = calc_lie(ld, fr->ener, lie_lj, lie_qq, fac_lj, fac_qq);
+ lieaver += lie;
+ lieav2 += lie*lie;
+ nframes++;
+ fprintf(out, "%10g %10g\n", fr->t, lie);
+ }
+ }
+ close_enx(fp);
+ gmx_ffclose(out);
+ fprintf(stderr, "\n");
+
+ if (nframes > 0)
+ {
+ printf("DGbind = %.3f (%.3f)\n", lieaver/nframes,
+ sqrt(lieav2/nframes-sqr(lieaver/nframes)));
+ }
+
+ do_view(oenv, ftp2fn(efXVG, NFILE, fnm), "-nxy");
+
+ return 0;
+}
--- /dev/null
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
+ * Copyright (c) 2001-2004, The GROMACS development team.
+ * Copyright (c) 2013,2014, by the GROMACS development team, led by
+ * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+ * and including many others, as listed in the AUTHORS file in the
+ * top-level source directory and at http://www.gromacs.org.
+ *
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
+ * of the License, or (at your option) any later version.
+ *
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+ *
+ * If you want to redistribute modifications to GROMACS, please
+ * consider that scientific software is very special. Version
+ * control is crucial - bugs must be traceable. We will be happy to
+ * consider code for inclusion in the official distribution, but
+ * derived work must not be called official GROMACS. Details are found
+ * in the README & COPYING files - if they are missing, get the
+ * official version at http://www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the research papers on the package. Check out http://www.gromacs.org.
+ */
+#include "addconf.h"
+
+#ifdef HAVE_CONFIG_H
+#include <config.h>
+#endif
+
+#include <stdlib.h>
+#include <string.h>
+#include "vec.h"
+#include "macros.h"
+#include "gromacs/utility/smalloc.h"
+#include "types/commrec.h"
+#include "force.h"
+#include "names.h"
+#include "nsgrid.h"
+#include "mdatoms.h"
+#include "nrnb.h"
+#include "ns.h"
+#include "mtop_util.h"
+#include "chargegroup.h"
+
+static real box_margin;
+
+static real max_dist(rvec *x, real *r, int start, int end)
+{
+ real maxd;
+ int i, j;
+
+ maxd = 0;
+ for (i = start; i < end; i++)
+ {
+ for (j = i+1; j < end; j++)
+ {
+ maxd = max(maxd, sqrt(distance2(x[i], x[j]))+0.5*(r[i]+r[j]));
+ }
+ }
+
+ return 0.5*maxd;
+}
+
+static gmx_bool outside_box_minus_margin2(rvec x, matrix box)
+{
+ return ( (x[XX] < 2*box_margin) || (x[XX] > box[XX][XX]-2*box_margin) ||
+ (x[YY] < 2*box_margin) || (x[YY] > box[YY][YY]-2*box_margin) ||
+ (x[ZZ] < 2*box_margin) || (x[ZZ] > box[ZZ][ZZ]-2*box_margin) );
+}
+
+static gmx_bool outside_box_plus_margin(rvec x, matrix box)
+{
+ return ( (x[XX] < -box_margin) || (x[XX] > box[XX][XX]+box_margin) ||
+ (x[YY] < -box_margin) || (x[YY] > box[YY][YY]+box_margin) ||
+ (x[ZZ] < -box_margin) || (x[ZZ] > box[ZZ][ZZ]+box_margin) );
+}
+
+static int mark_res(int at, gmx_bool *mark, int natoms, t_atom *atom, int *nmark)
+{
+ int resind;
+
+ resind = atom[at].resind;
+ while ( (at > 0) && (resind == atom[at-1].resind) )
+ {
+ at--;
+ }
+ while ( (at < natoms) && (resind == atom[at].resind) )
+ {
+ if (!mark[at])
+ {
+ mark[at] = TRUE;
+ (*nmark)++;
+ }
+ at++;
+ }
+
+ return at;
+}
+
+static real find_max_real(int n, real radius[])
+{
+ int i;
+ real rmax;
+
+ rmax = 0;
+ if (n > 0)
+ {
+ rmax = radius[0];
+ for (i = 1; (i < n); i++)
+ {
+ rmax = max(rmax, radius[i]);
+ }
+ }
+ return rmax;
+}
+
+static void combine_atoms(t_atoms *ap, t_atoms *as,
+ rvec xp[], rvec *vp, rvec xs[], rvec *vs,
+ t_atoms **a_comb, rvec **x_comb, rvec **v_comb)
+{
+ t_atoms *ac;
+ rvec *xc, *vc = NULL;
+ int i, j, natot, res0;
+
+ /* Total number of atoms */
+ natot = ap->nr+as->nr;
+
+ snew(ac, 1);
+ init_t_atoms(ac, natot, FALSE);
+
+ snew(xc, natot);
+ if (vp && vs)
+ {
+ snew(vc, natot);
+ }
+
+ /* Fill the new structures */
+ for (i = j = 0; (i < ap->nr); i++, j++)
+ {
+ copy_rvec(xp[i], xc[j]);
+ if (vc)
+ {
+ copy_rvec(vp[i], vc[j]);
+ }
+ memcpy(&(ac->atom[j]), &(ap->atom[i]), sizeof(ap->atom[i]));
+ ac->atom[j].type = 0;
+ }
+ res0 = ap->nres;
+ for (i = 0; (i < as->nr); i++, j++)
+ {
+ copy_rvec(xs[i], xc[j]);
+ if (vc)
+ {
+ copy_rvec(vs[i], vc[j]);
+ }
+ memcpy(&(ac->atom[j]), &(as->atom[i]), sizeof(as->atom[i]));
+ ac->atom[j].type = 0;
+ ac->atom[j].resind += res0;
+ }
+ ac->nr = j;
+ ac->nres = ac->atom[j-1].resind+1;
+ /* Fill all elements to prevent uninitialized memory */
+ for (i = 0; i < ac->nr; i++)
+ {
+ ac->atom[i].m = 1;
+ ac->atom[i].q = 0;
+ ac->atom[i].mB = 1;
+ ac->atom[i].qB = 0;
+ ac->atom[i].type = 0;
+ ac->atom[i].typeB = 0;
+ ac->atom[i].ptype = eptAtom;
+ }
+
+ /* Return values */
+ *a_comb = ac;
+ *x_comb = xc;
+ *v_comb = vc;
+}
+
+static t_forcerec *fr = NULL;
+
+static void do_nsgrid(FILE *fp, gmx_bool bVerbose,
+ matrix box, rvec x[], t_atoms *atoms, real rlong,
+ const output_env_t oenv)
+{
+ gmx_mtop_t *mtop;
+ gmx_localtop_t *top;
+ t_mdatoms *md;
+ t_block *cgs;
+ t_inputrec *ir;
+ t_nrnb nrnb;
+ t_commrec *cr;
+ int *cg_index;
+ gmx_moltype_t *molt;
+ gmx_ffparams_t *ffp;
+ ivec *nFreeze;
+ int i, m, natoms;
+ rvec box_size;
+ real *lambda, *dvdl;
+
+ natoms = atoms->nr;
+
+ /* Charge group index */
+ snew(cg_index, natoms);
+ for (i = 0; (i < natoms); i++)
+ {
+ cg_index[i] = i;
+ }
+
+ /* Topology needs charge groups and exclusions */
+ snew(mtop, 1);
+ init_mtop(mtop);
+ mtop->natoms = natoms;
+ /* Make one moltype that contains the whol system */
+ mtop->nmoltype = 1;
+ snew(mtop->moltype, mtop->nmoltype);
+ molt = &mtop->moltype[0];
+ molt->name = mtop->name;
+ molt->atoms = *atoms;
+ stupid_fill_block(&molt->cgs, mtop->natoms, FALSE);
+ stupid_fill_blocka(&molt->excls, natoms);
+ /* Make one molblock for the whole system */
+ mtop->nmolblock = 1;
+ snew(mtop->molblock, mtop->nmolblock);
+ mtop->molblock[0].type = 0;
+ mtop->molblock[0].nmol = 1;
+ mtop->molblock[0].natoms_mol = natoms;
+ /* Initialize a single energy group */
+ mtop->groups.grps[egcENER].nr = 1;
+ mtop->groups.ngrpnr[egcENER] = 0;
+ mtop->groups.grpnr[egcENER] = NULL;
+
+ ffp = &mtop->ffparams;
+
+ ffp->ntypes = 1;
+ ffp->atnr = 1;
+ ffp->reppow = 12;
+ snew(ffp->functype, 1);
+ snew(ffp->iparams, 1);
+ ffp->iparams[0].lj.c6 = 1;
+ ffp->iparams[0].lj.c12 = 1;
+
+ /* inputrec structure */
+ snew(ir, 1);
+ ir->cutoff_scheme = ecutsGROUP;
+ ir->coulomb_modifier = eintmodNONE;
+ ir->vdw_modifier = eintmodNONE;
+ ir->coulombtype = eelCUT;
+ ir->vdwtype = evdwCUT;
+ ir->ndelta = 2;
+ ir->ns_type = ensGRID;
+ snew(ir->opts.egp_flags, 1);
+
+ top = gmx_mtop_generate_local_top(mtop, ir);
+
+ /* Some nasty shortcuts */
+ cgs = &(top->cgs);
+
+ /* mdatoms structure */
+ snew(nFreeze, 2);
+ snew(md, 1);
+ md = init_mdatoms(fp, mtop, FALSE);
+ atoms2md(mtop, ir, 0, NULL, mtop->natoms, md);
+ sfree(nFreeze);
+
+ /* forcerec structure */
+ if (fr == NULL)
+ {
+ fr = mk_forcerec();
+ }
+ snew(cr, 1);
+ cr->nnodes = 1;
+ /* cr->nthreads = 1; */
+
+ /* ir->rlist = ir->rcoulomb = ir->rvdw = rlong;
+ printf("Neighborsearching with a cut-off of %g\n",rlong);
+ init_forcerec(stdout,fr,ir,top,cr,md,box,FALSE,NULL,NULL,NULL,TRUE);*/
+ fr->cg0 = 0;
+ fr->hcg = top->cgs.nr;
+ fr->nWatMol = 0;
+
+ /* Prepare for neighboursearching */
+ init_nrnb(&nrnb);
+
+ /* Init things dependent on parameters */
+ ir->rlistlong = ir->rlist = ir->rcoulomb = ir->rvdw = rlong;
+ /* create free energy data to avoid NULLs */
+ snew(ir->fepvals, 1);
+ printf("Neighborsearching with a cut-off of %g\n", rlong);
+ init_forcerec(stdout, oenv, fr, NULL, ir, mtop, cr, box,
+ NULL, NULL, NULL, NULL, NULL, TRUE, -1);
+ if (debug)
+ {
+ pr_forcerec(debug, fr);
+ }
+
+ /* Calculate new stuff dependent on coords and box */
+ for (m = 0; (m < DIM); m++)
+ {
+ box_size[m] = box[m][m];
+ }
+ calc_shifts(box, fr->shift_vec);
+ put_charge_groups_in_box(fp, 0, cgs->nr, fr->ePBC, box, cgs, x, fr->cg_cm);
+
+ /* Do the actual neighboursearching */
+ snew(lambda, efptNR);
+ snew(dvdl, efptNR);
+ init_neighbor_list(fp, fr, md->homenr);
+ search_neighbours(fp, fr, box, top,
+ &mtop->groups, cr, &nrnb, md, TRUE, FALSE);
+
+ if (debug)
+ {
+ dump_nblist(debug, cr, fr, 0);
+ }
+
+ if (bVerbose)
+ {
+ fprintf(stderr, "Successfully made neighbourlist\n");
+ }
+}
+
+static gmx_bool bXor(gmx_bool b1, gmx_bool b2)
+{
+ return (b1 && !b2) || (b2 && !b1);
+}
+
+void add_conf(t_atoms *atoms, rvec **x, rvec **v, real **r, gmx_bool bSrenew,
+ int ePBC, matrix box, gmx_bool bInsert,
+ t_atoms *atoms_solvt, rvec *x_solvt, rvec *v_solvt, real *r_solvt,
+ gmx_bool bVerbose, real rshell, int max_sol, const output_env_t oenv)
+{
+ t_nblist *nlist;
+ t_atoms *atoms_all;
+ real max_vdw, *r_prot, *r_all, n2, r2, ib1, ib2;
+ int natoms_prot, natoms_solvt;
+ int i, j, jj, m, j0, j1, jjj, jnres, jnr, inr, iprot, is1, is2;
+ int prev, resnr, nresadd, d, k, ncells, maxincell;
+ int dx0, dx1, dy0, dy1, dz0, dz1;
+ int ntest, nremove, nkeep;
+ rvec dx, xi, xj, xpp, *x_all, *v_all;
+ gmx_bool *remove, *keep;
+ int bSolSol;
+
+ natoms_prot = atoms->nr;
+ natoms_solvt = atoms_solvt->nr;
+ if (natoms_solvt <= 0)
+ {
+ fprintf(stderr, "WARNING: Nothing to add\n");
+ return;
+ }
+
+ if (ePBC == epbcSCREW)
+ {
+ gmx_fatal(FARGS, "Sorry, %s pbc is not yet supported", epbc_names[ePBC]);
+ }
+
+ if (bVerbose)
+ {
+ fprintf(stderr, "Calculating Overlap...\n");
+ }
+
+ /* Set margin around box edges to largest solvent dimension.
+ * The maximum distance between atoms in a solvent molecule should
+ * be calculated. At the moment a fudge factor of 3 is used.
+ */
+ r_prot = *r;
+ box_margin = 3*find_max_real(natoms_solvt, r_solvt);
+ max_vdw = max(3*find_max_real(natoms_prot, r_prot), box_margin);
+ fprintf(stderr, "box_margin = %g\n", box_margin);
+
+ snew(remove, natoms_solvt);
+
+ nremove = 0;
+ if (!bInsert)
+ {
+ for (i = 0; i < atoms_solvt->nr; i++)
+ {
+ if (outside_box_plus_margin(x_solvt[i], box) )
+ {
+ i = mark_res(i, remove, atoms_solvt->nr, atoms_solvt->atom, &nremove);
+ }
+ }
+ fprintf(stderr, "Removed %d atoms that were outside the box\n", nremove);
+ }
+
+ /* Define grid stuff */
+ /* Largest VDW radius */
+ snew(r_all, natoms_prot+natoms_solvt);
+ for (i = j = 0; i < natoms_prot; i++, j++)
+ {
+ r_all[j] = r_prot[i];
+ }
+ for (i = 0; i < natoms_solvt; i++, j++)
+ {
+ r_all[j] = r_solvt[i];
+ }
+
+ /* Combine arrays */
+ combine_atoms(atoms, atoms_solvt, *x, v ? *v : NULL, x_solvt, v_solvt,
+ &atoms_all, &x_all, &v_all);
+
+ /* Do neighboursearching step */
+ do_nsgrid(stdout, bVerbose, box, x_all, atoms_all, max_vdw, oenv);
+
+ /* check solvent with solute */
+ nlist = &(fr->nblists[0].nlist_sr[eNL_VDW]);
+ fprintf(stderr, "nri = %d, nrj = %d\n", nlist->nri, nlist->nrj);
+ for (bSolSol = 0; (bSolSol <= (bInsert ? 0 : 1)); bSolSol++)
+ {
+ ntest = nremove = 0;
+ fprintf(stderr, "Checking %s-Solvent overlap:",
+ bSolSol ? "Solvent" : "Protein");
+ for (i = 0; (i < nlist->nri && nremove < natoms_solvt); i++)
+ {
+ inr = nlist->iinr[i];
+ j0 = nlist->jindex[i];
+ j1 = nlist->jindex[i+1];
+ rvec_add(x_all[inr], fr->shift_vec[nlist->shift[i]], xi);
+
+ for (j = j0; (j < j1 && nremove < natoms_solvt); j++)
+ {
+ jnr = nlist->jjnr[j];
++ if (jnr < 0)
++ {
++ /* skip padding */
++ continue;
++ }
+ copy_rvec(x_all[jnr], xj);
+
+ /* Check solvent-protein and solvent-solvent */
+ is1 = inr-natoms_prot;
+ is2 = jnr-natoms_prot;
+
+ /* Check if at least one of the atoms is a solvent that is not yet
+ * listed for removal, and if both are solvent, that they are not in the
+ * same residue.
+ */
+ if ((!bSolSol &&
+ bXor((is1 >= 0), (is2 >= 0)) && /* One atom is protein */
+ ((is1 < 0) || ((is1 >= 0) && !remove[is1])) &&
+ ((is2 < 0) || ((is2 >= 0) && !remove[is2]))) ||
+
+ (bSolSol &&
+ (is1 >= 0) && (!remove[is1]) && /* is1 is solvent */
+ (is2 >= 0) && (!remove[is2]) && /* is2 is solvent */
+ (bInsert || /* when inserting also check inside the box */
+ (outside_box_minus_margin2(x_solvt[is1], box) && /* is1 on edge */
+ outside_box_minus_margin2(x_solvt[is2], box)) /* is2 on edge */
+ ) &&
+ (atoms_solvt->atom[is1].resind != /* Not the same residue */
+ atoms_solvt->atom[is2].resind)))
+ {
+
+ ntest++;
+ rvec_sub(xi, xj, dx);
+ n2 = norm2(dx);
+ r2 = sqr(r_all[inr]+r_all[jnr]);
+ if (n2 < r2)
+ {
+ if (bInsert)
+ {
+ nremove = natoms_solvt;
+ for (k = 0; k < nremove; k++)
+ {
+ remove[k] = TRUE;
+ }
+ }
+ /* Need only remove one of the solvents... */
+ if (is2 >= 0)
+ {
+ (void) mark_res(is2, remove, natoms_solvt, atoms_solvt->atom,
+ &nremove);
+ }
+ else if (is1 >= 0)
+ {
+ (void) mark_res(is1, remove, natoms_solvt, atoms_solvt->atom,
+ &nremove);
+ }
+ else
+ {
+ fprintf(stderr, "Neither atom is solvent%d %d\n", is1, is2);
+ }
+ }
+ }
+ }
+ }
+ if (!bInsert)
+ {
+ fprintf(stderr, " tested %d pairs, removed %d atoms.\n", ntest, nremove);
+ }
+ }
+ if (debug)
+ {
+ for (i = 0; i < natoms_solvt; i++)
+ {
+ fprintf(debug, "remove[%5d] = %s\n", i, bool_names[remove[i]]);
+ }
+ }
+
+ /* Search again, now with another cut-off */
+ if (rshell > 0)
+ {
+ do_nsgrid(stdout, bVerbose, box, x_all, atoms_all, rshell, oenv);
+ nlist = &(fr->nblists[0].nlist_sr[eNL_VDW]);
+ fprintf(stderr, "nri = %d, nrj = %d\n", nlist->nri, nlist->nrj);
+ nkeep = 0;
+ snew(keep, natoms_solvt);
+ for (i = 0; i < nlist->nri; i++)
+ {
+ inr = nlist->iinr[i];
+ j0 = nlist->jindex[i];
+ j1 = nlist->jindex[i+1];
+
+ for (j = j0; j < j1; j++)
+ {
+ jnr = nlist->jjnr[j];
+
+ /* Check solvent-protein and solvent-solvent */
+ is1 = inr-natoms_prot;
+ is2 = jnr-natoms_prot;
+
+ /* Check if at least one of the atoms is a solvent that is not yet
+ * listed for removal, and if both are solvent, that they are not in the
+ * same residue.
+ */
+ if (is1 >= 0 && is2 < 0)
+ {
+ mark_res(is1, keep, natoms_solvt, atoms_solvt->atom, &nkeep);
+ }
+ else if (is1 < 0 && is2 >= 0)
+ {
+ mark_res(is2, keep, natoms_solvt, atoms_solvt->atom, &nkeep);
+ }
+ }
+ }
+ fprintf(stderr, "Keeping %d solvent atoms after proximity check\n",
+ nkeep);
+ for (i = 0; i < natoms_solvt; i++)
+ {
+ remove[i] = remove[i] || !keep[i];
+ }
+ sfree(keep);
+ }
+ /* count how many atoms and residues will be added and make space */
+ if (bInsert)
+ {
+ j = atoms_solvt->nr;
+ jnres = atoms_solvt->nres;
+ }
+ else
+ {
+ j = 0;
+ jnres = 0;
+ for (i = 0; ((i < atoms_solvt->nr) &&
+ ((max_sol == 0) || (jnres < max_sol))); i++)
+ {
+ if (!remove[i])
+ {
+ j++;
+ if ((i == 0) ||
+ (atoms_solvt->atom[i].resind != atoms_solvt->atom[i-1].resind))
+ {
+ jnres++;
+ }
+ }
+ }
+ }
+ if (debug)
+ {
+ fprintf(debug, "Will add %d atoms in %d residues\n", j, jnres);
+ }
+ if (!bInsert)
+ {
+ /* Flag the remaing solvent atoms to be removed */
+ jjj = atoms_solvt->atom[i-1].resind;
+ for (; (i < atoms_solvt->nr); i++)
+ {
+ if (atoms_solvt->atom[i].resind > jjj)
+ {
+ remove[i] = TRUE;
+ }
+ else
+ {
+ j++;
+ }
+ }
+ }
+
+ if (bSrenew)
+ {
+ srenew(atoms->resinfo, atoms->nres+jnres);
+ srenew(atoms->atomname, atoms->nr+j);
+ srenew(atoms->atom, atoms->nr+j);
+ srenew(*x, atoms->nr+j);
+ if (v)
+ {
+ srenew(*v, atoms->nr+j);
+ }
+ srenew(*r, atoms->nr+j);
+ }
+
+ /* add the selected atoms_solvt to atoms */
+ if (atoms->nr > 0)
+ {
+ resnr = atoms->resinfo[atoms->atom[atoms->nr-1].resind].nr;
+ }
+ else
+ {
+ resnr = 0;
+ }
+ prev = -1;
+ nresadd = 0;
+ for (i = 0; i < atoms_solvt->nr; i++)
+ {
+ if (!remove[i])
+ {
+ if (prev == -1 ||
+ atoms_solvt->atom[i].resind != atoms_solvt->atom[prev].resind)
+ {
+ nresadd++;
+ atoms->nres++;
+ resnr++;
+ atoms->resinfo[atoms->nres-1] =
+ atoms_solvt->resinfo[atoms_solvt->atom[i].resind];
+ atoms->resinfo[atoms->nres-1].nr = resnr;
+ /* calculate shift of the solvent molecule using the first atom */
+ copy_rvec(x_solvt[i], dx);
+ put_atoms_in_box(ePBC, box, 1, &dx);
+ rvec_dec(dx, x_solvt[i]);
+ }
+ atoms->atom[atoms->nr] = atoms_solvt->atom[i];
+ atoms->atomname[atoms->nr] = atoms_solvt->atomname[i];
+ rvec_add(x_solvt[i], dx, (*x)[atoms->nr]);
+ if (v)
+ {
+ copy_rvec(v_solvt[i], (*v)[atoms->nr]);
+ }
+ (*r)[atoms->nr] = r_solvt[i];
+ atoms->atom[atoms->nr].resind = atoms->nres-1;
+ atoms->nr++;
+ prev = i;
+ }
+ }
+ if (bSrenew)
+ {
+ srenew(atoms->resinfo, atoms->nres+nresadd);
+ }
+
+ if (bVerbose)
+ {
+ fprintf(stderr, "Added %d molecules\n", nresadd);
+ }
+
+ sfree(remove);
+ done_atom(atoms_all);
+ sfree(x_all);
+ sfree(v_all);
+}
--- /dev/null
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
+ * Copyright (c) 2001-2004, The GROMACS development team.
+ * Copyright (c) 2013,2014, by the GROMACS development team, led by
+ * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+ * and including many others, as listed in the AUTHORS file in the
+ * top-level source directory and at http://www.gromacs.org.
+ *
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
+ * of the License, or (at your option) any later version.
+ *
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+ *
+ * If you want to redistribute modifications to GROMACS, please
+ * consider that scientific software is very special. Version
+ * control is crucial - bugs must be traceable. We will be happy to
+ * consider code for inclusion in the official distribution, but
+ * derived work must not be called official GROMACS. Details are found
+ * in the README & COPYING files - if they are missing, get the
+ * official version at http://www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the research papers on the package. Check out http://www.gromacs.org.
+ */
+#include "grompp.h"
+
+#ifdef HAVE_CONFIG_H
+#include <config.h>
+#endif
+
+#include <sys/types.h>
+#include <math.h>
+#include <string.h>
+#include <errno.h>
+#include <limits.h>
+#include <assert.h>
+
+#include "sysstuff.h"
+#include "gromacs/utility/smalloc.h"
+#include "macros.h"
+#include "readir.h"
+#include "toputil.h"
+#include "topio.h"
+#include "gromacs/fileio/confio.h"
+#include "readir.h"
+#include "symtab.h"
+#include "names.h"
+#include "grompp-impl.h"
+#include "gromacs/random/random.h"
+#include "gromacs/gmxpreprocess/gen_maxwell_velocities.h"
+#include "vec.h"
+#include "gromacs/fileio/futil.h"
+#include "gromacs/commandline/pargs.h"
+#include "splitter.h"
+#include "gromacs/gmxpreprocess/sortwater.h"
+#include "convparm.h"
+#include "gmx_fatal.h"
+#include "warninp.h"
+#include "index.h"
+#include "gromacs/fileio/gmxfio.h"
+#include "gromacs/fileio/trnio.h"
+#include "gromacs/fileio/tpxio.h"
+#include "gromacs/fileio/trxio.h"
+#include "vsite_parm.h"
+#include "txtdump.h"
+#include "calcgrid.h"
+#include "add_par.h"
+#include "gromacs/fileio/enxio.h"
+#include "perf_est.h"
+#include "compute_io.h"
+#include "gpp_atomtype.h"
+#include "mtop_util.h"
+#include "genborn.h"
+#include "calc_verletbuf.h"
+#include "tomorse.h"
+#include "gromacs/imd/imd.h"
+
+
+static int rm_interactions(int ifunc, int nrmols, t_molinfo mols[])
+{
+ int i, n;
+
+ n = 0;
+ /* For all the molecule types */
+ for (i = 0; i < nrmols; i++)
+ {
+ n += mols[i].plist[ifunc].nr;
+ mols[i].plist[ifunc].nr = 0;
+ }
+ return n;
+}
+
+static int check_atom_names(const char *fn1, const char *fn2,
+ gmx_mtop_t *mtop, t_atoms *at)
+{
+ int mb, m, i, j, nmismatch;
+ t_atoms *tat;
+#define MAXMISMATCH 20
+
+ if (mtop->natoms != at->nr)
+ {
+ gmx_incons("comparing atom names");
+ }
+
+ nmismatch = 0;
+ i = 0;
+ for (mb = 0; mb < mtop->nmolblock; mb++)
+ {
+ tat = &mtop->moltype[mtop->molblock[mb].type].atoms;
+ for (m = 0; m < mtop->molblock[mb].nmol; m++)
+ {
+ for (j = 0; j < tat->nr; j++)
+ {
+ if (strcmp( *(tat->atomname[j]), *(at->atomname[i]) ) != 0)
+ {
+ if (nmismatch < MAXMISMATCH)
+ {
+ fprintf(stderr,
+ "Warning: atom name %d in %s and %s does not match (%s - %s)\n",
+ i+1, fn1, fn2, *(tat->atomname[j]), *(at->atomname[i]));
+ }
+ else if (nmismatch == MAXMISMATCH)
+ {
+ fprintf(stderr, "(more than %d non-matching atom names)\n", MAXMISMATCH);
+ }
+ nmismatch++;
+ }
+ i++;
+ }
+ }
+ }
+
+ return nmismatch;
+}
+
+static void check_eg_vs_cg(gmx_mtop_t *mtop)
+{
+ int astart, mb, m, cg, j, firstj;
+ unsigned char firsteg, eg;
+ gmx_moltype_t *molt;
+
+ /* Go through all the charge groups and make sure all their
+ * atoms are in the same energy group.
+ */
+
+ astart = 0;
+ for (mb = 0; mb < mtop->nmolblock; mb++)
+ {
+ molt = &mtop->moltype[mtop->molblock[mb].type];
+ for (m = 0; m < mtop->molblock[mb].nmol; m++)
+ {
+ for (cg = 0; cg < molt->cgs.nr; cg++)
+ {
+ /* Get the energy group of the first atom in this charge group */
+ firstj = astart + molt->cgs.index[cg];
+ firsteg = ggrpnr(&mtop->groups, egcENER, firstj);
+ for (j = molt->cgs.index[cg]+1; j < molt->cgs.index[cg+1]; j++)
+ {
+ eg = ggrpnr(&mtop->groups, egcENER, astart+j);
+ if (eg != firsteg)
+ {
+ gmx_fatal(FARGS, "atoms %d and %d in charge group %d of molecule type '%s' are in different energy groups",
+ firstj+1, astart+j+1, cg+1, *molt->name);
+ }
+ }
+ }
+ astart += molt->atoms.nr;
+ }
+ }
+}
+
+static void check_cg_sizes(const char *topfn, t_block *cgs, warninp_t wi)
+{
+ int maxsize, cg;
+ char warn_buf[STRLEN];
+
+ maxsize = 0;
+ for (cg = 0; cg < cgs->nr; cg++)
+ {
+ maxsize = max(maxsize, cgs->index[cg+1]-cgs->index[cg]);
+ }
+
+ if (maxsize > MAX_CHARGEGROUP_SIZE)
+ {
+ gmx_fatal(FARGS, "The largest charge group contains %d atoms. The maximum is %d.", maxsize, MAX_CHARGEGROUP_SIZE);
+ }
+ else if (maxsize > 10)
+ {
+ set_warning_line(wi, topfn, -1);
+ sprintf(warn_buf,
+ "The largest charge group contains %d atoms.\n"
+ "Since atoms only see each other when the centers of geometry of the charge groups they belong to are within the cut-off distance, too large charge groups can lead to serious cut-off artifacts.\n"
+ "For efficiency and accuracy, charge group should consist of a few atoms.\n"
+ "For all-atom force fields use: CH3, CH2, CH, NH2, NH, OH, CO2, CO, etc.",
+ maxsize);
+ warning_note(wi, warn_buf);
+ }
+}
+
+static void check_bonds_timestep(gmx_mtop_t *mtop, double dt, warninp_t wi)
+{
+ /* This check is not intended to ensure accurate integration,
+ * rather it is to signal mistakes in the mdp settings.
+ * A common mistake is to forget to turn on constraints
+ * for MD after energy minimization with flexible bonds.
+ * This check can also detect too large time steps for flexible water
+ * models, but such errors will often be masked by the constraints
+ * mdp options, which turns flexible water into water with bond constraints,
+ * but without an angle constraint. Unfortunately such incorrect use
+ * of water models can not easily be detected without checking
+ * for specific model names.
+ *
+ * The stability limit of leap-frog or velocity verlet is 4.44 steps
+ * per oscillational period.
+ * But accurate bonds distributions are lost far before that limit.
+ * To allow relatively common schemes (although not common with Gromacs)
+ * of dt=1 fs without constraints and dt=2 fs with only H-bond constraints
+ * we set the note limit to 10.
+ */
+ int min_steps_warn = 5;
+ int min_steps_note = 10;
+ t_iparams *ip;
+ int molt;
+ gmx_moltype_t *moltype, *w_moltype;
+ t_atom *atom;
+ t_ilist *ilist, *ilb, *ilc, *ils;
+ int ftype;
+ int i, a1, a2, w_a1, w_a2, j;
+ real twopi2, limit2, fc, re, m1, m2, period2, w_period2;
+ gmx_bool bFound, bWater, bWarn;
+ char warn_buf[STRLEN];
+
+ ip = mtop->ffparams.iparams;
+
+ twopi2 = sqr(2*M_PI);
+
+ limit2 = sqr(min_steps_note*dt);
+
+ w_a1 = w_a2 = -1;
+ w_period2 = -1.0;
+
+ w_moltype = NULL;
+ for (molt = 0; molt < mtop->nmoltype; molt++)
+ {
+ moltype = &mtop->moltype[molt];
+ atom = moltype->atoms.atom;
+ ilist = moltype->ilist;
+ ilc = &ilist[F_CONSTR];
+ ils = &ilist[F_SETTLE];
+ for (ftype = 0; ftype < F_NRE; ftype++)
+ {
+ if (!(ftype == F_BONDS || ftype == F_G96BONDS || ftype == F_HARMONIC))
+ {
+ continue;
+ }
+
+ ilb = &ilist[ftype];
+ for (i = 0; i < ilb->nr; i += 3)
+ {
+ fc = ip[ilb->iatoms[i]].harmonic.krA;
+ re = ip[ilb->iatoms[i]].harmonic.rA;
+ if (ftype == F_G96BONDS)
+ {
+ /* Convert squared sqaure fc to harmonic fc */
+ fc = 2*fc*re;
+ }
+ a1 = ilb->iatoms[i+1];
+ a2 = ilb->iatoms[i+2];
+ m1 = atom[a1].m;
+ m2 = atom[a2].m;
+ if (fc > 0 && m1 > 0 && m2 > 0)
+ {
+ period2 = twopi2*m1*m2/((m1 + m2)*fc);
+ }
+ else
+ {
+ period2 = GMX_FLOAT_MAX;
+ }
+ if (debug)
+ {
+ fprintf(debug, "fc %g m1 %g m2 %g period %g\n",
+ fc, m1, m2, sqrt(period2));
+ }
+ if (period2 < limit2)
+ {
+ bFound = FALSE;
+ for (j = 0; j < ilc->nr; j += 3)
+ {
+ if ((ilc->iatoms[j+1] == a1 && ilc->iatoms[j+2] == a2) ||
+ (ilc->iatoms[j+1] == a2 && ilc->iatoms[j+2] == a1))
+ {
+ bFound = TRUE;
+ }
+ }
+ for (j = 0; j < ils->nr; j += 4)
+ {
+ if ((a1 == ils->iatoms[j+1] || a1 == ils->iatoms[j+2] || a1 == ils->iatoms[j+3]) &&
+ (a2 == ils->iatoms[j+1] || a2 == ils->iatoms[j+2] || a2 == ils->iatoms[j+3]))
+ {
+ bFound = TRUE;
+ }
+ }
+ if (!bFound &&
+ (w_moltype == NULL || period2 < w_period2))
+ {
+ w_moltype = moltype;
+ w_a1 = a1;
+ w_a2 = a2;
+ w_period2 = period2;
+ }
+ }
+ }
+ }
+ }
+
+ if (w_moltype != NULL)
+ {
+ bWarn = (w_period2 < sqr(min_steps_warn*dt));
+ /* A check that would recognize most water models */
+ bWater = ((*w_moltype->atoms.atomname[0])[0] == 'O' &&
+ w_moltype->atoms.nr <= 5);
+ sprintf(warn_buf, "The bond in molecule-type %s between atoms %d %s and %d %s has an estimated oscillational period of %.1e ps, which is less than %d times the time step of %.1e ps.\n"
+ "%s",
+ *w_moltype->name,
+ w_a1+1, *w_moltype->atoms.atomname[w_a1],
+ w_a2+1, *w_moltype->atoms.atomname[w_a2],
+ sqrt(w_period2), bWarn ? min_steps_warn : min_steps_note, dt,
+ bWater ?
+ "Maybe you asked for fexible water." :
+ "Maybe you forgot to change the constraints mdp option.");
+ if (bWarn)
+ {
+ warning(wi, warn_buf);
+ }
+ else
+ {
+ warning_note(wi, warn_buf);
+ }
+ }
+}
+
+static void check_vel(gmx_mtop_t *mtop, rvec v[])
+{
+ gmx_mtop_atomloop_all_t aloop;
+ t_atom *atom;
+ int a;
+
+ aloop = gmx_mtop_atomloop_all_init(mtop);
+ while (gmx_mtop_atomloop_all_next(aloop, &a, &atom))
+ {
+ if (atom->ptype == eptShell ||
+ atom->ptype == eptBond ||
+ atom->ptype == eptVSite)
+ {
+ clear_rvec(v[a]);
+ }
+ }
+}
+
+static gmx_bool nint_ftype(gmx_mtop_t *mtop, t_molinfo *mi, int ftype)
+{
+ int nint, mb;
+
+ nint = 0;
+ for (mb = 0; mb < mtop->nmolblock; mb++)
+ {
+ nint += mtop->molblock[mb].nmol*mi[mtop->molblock[mb].type].plist[ftype].nr;
+ }
+
+ return nint;
+}
+
+/* This routine reorders the molecule type array
+ * in the order of use in the molblocks,
+ * unused molecule types are deleted.
+ */
+static void renumber_moltypes(gmx_mtop_t *sys,
+ int *nmolinfo, t_molinfo **molinfo)
+{
+ int *order, norder, i;
+ int mb, mi;
+ t_molinfo *minew;
+
+ snew(order, *nmolinfo);
+ norder = 0;
+ for (mb = 0; mb < sys->nmolblock; mb++)
+ {
+ for (i = 0; i < norder; i++)
+ {
+ if (order[i] == sys->molblock[mb].type)
+ {
+ break;
+ }
+ }
+ if (i == norder)
+ {
+ /* This type did not occur yet, add it */
+ order[norder] = sys->molblock[mb].type;
+ /* Renumber the moltype in the topology */
+ norder++;
+ }
+ sys->molblock[mb].type = i;
+ }
+
+ /* We still need to reorder the molinfo structs */
+ snew(minew, norder);
+ for (mi = 0; mi < *nmolinfo; mi++)
+ {
+ for (i = 0; i < norder; i++)
+ {
+ if (order[i] == mi)
+ {
+ break;
+ }
+ }
+ if (i == norder)
+ {
+ done_mi(&(*molinfo)[mi]);
+ }
+ else
+ {
+ minew[i] = (*molinfo)[mi];
+ }
+ }
+ sfree(*molinfo);
+
+ *nmolinfo = norder;
+ *molinfo = minew;
+}
+
+static void molinfo2mtop(int nmi, t_molinfo *mi, gmx_mtop_t *mtop)
+{
+ int m;
+ gmx_moltype_t *molt;
+
+ mtop->nmoltype = nmi;
+ snew(mtop->moltype, nmi);
+ for (m = 0; m < nmi; m++)
+ {
+ molt = &mtop->moltype[m];
+ molt->name = mi[m].name;
+ molt->atoms = mi[m].atoms;
+ /* ilists are copied later */
+ molt->cgs = mi[m].cgs;
+ molt->excls = mi[m].excls;
+ }
+}
+
+static void
+new_status(const char *topfile, const char *topppfile, const char *confin,
+ t_gromppopts *opts, t_inputrec *ir, gmx_bool bZero,
+ gmx_bool bGenVel, gmx_bool bVerbose, t_state *state,
+ gpp_atomtype_t atype, gmx_mtop_t *sys,
+ int *nmi, t_molinfo **mi, t_params plist[],
+ int *comb, double *reppow, real *fudgeQQ,
+ gmx_bool bMorse,
+ warninp_t wi)
+{
+ t_molinfo *molinfo = NULL;
+ int nmolblock;
+ gmx_molblock_t *molblock, *molbs;
+ t_atoms *confat;
+ int mb, i, nrmols, nmismatch;
+ char buf[STRLEN];
+ gmx_bool bGB = FALSE;
+ char warn_buf[STRLEN];
+
+ init_mtop(sys);
+
+ /* Set gmx_boolean for GB */
+ if (ir->implicit_solvent)
+ {
+ bGB = TRUE;
+ }
+
+ /* TOPOLOGY processing */
+ sys->name = do_top(bVerbose, topfile, topppfile, opts, bZero, &(sys->symtab),
+ plist, comb, reppow, fudgeQQ,
+ atype, &nrmols, &molinfo, ir,
+ &nmolblock, &molblock, bGB,
+ wi);
+
+ sys->nmolblock = 0;
+ snew(sys->molblock, nmolblock);
+
+ sys->natoms = 0;
+ for (mb = 0; mb < nmolblock; mb++)
+ {
+ if (sys->nmolblock > 0 &&
+ molblock[mb].type == sys->molblock[sys->nmolblock-1].type)
+ {
+ /* Merge consecutive blocks with the same molecule type */
+ sys->molblock[sys->nmolblock-1].nmol += molblock[mb].nmol;
+ sys->natoms += molblock[mb].nmol*sys->molblock[sys->nmolblock-1].natoms_mol;
+ }
+ else if (molblock[mb].nmol > 0)
+ {
+ /* Add a new molblock to the topology */
+ molbs = &sys->molblock[sys->nmolblock];
+ *molbs = molblock[mb];
+ molbs->natoms_mol = molinfo[molbs->type].atoms.nr;
+ molbs->nposres_xA = 0;
+ molbs->nposres_xB = 0;
+ sys->natoms += molbs->nmol*molbs->natoms_mol;
+ sys->nmolblock++;
+ }
+ }
+ if (sys->nmolblock == 0)
+ {
+ gmx_fatal(FARGS, "No molecules were defined in the system");
+ }
+
+ renumber_moltypes(sys, &nrmols, &molinfo);
+
+ if (bMorse)
+ {
+ convert_harmonics(nrmols, molinfo, atype);
+ }
+
+ if (ir->eDisre == edrNone)
+ {
+ i = rm_interactions(F_DISRES, nrmols, molinfo);
+ if (i > 0)
+ {
+ set_warning_line(wi, "unknown", -1);
+ sprintf(warn_buf, "disre = no, removed %d distance restraints", i);
+ warning_note(wi, warn_buf);
+ }
+ }
+ if (opts->bOrire == FALSE)
+ {
+ i = rm_interactions(F_ORIRES, nrmols, molinfo);
+ if (i > 0)
+ {
+ set_warning_line(wi, "unknown", -1);
+ sprintf(warn_buf, "orire = no, removed %d orientation restraints", i);
+ warning_note(wi, warn_buf);
+ }
+ }
+
+ /* Copy structures from msys to sys */
+ molinfo2mtop(nrmols, molinfo, sys);
+
+ gmx_mtop_finalize(sys);
+
+ /* COORDINATE file processing */
+ if (bVerbose)
+ {
+ fprintf(stderr, "processing coordinates...\n");
+ }
+
+ get_stx_coordnum(confin, &state->natoms);
+ if (state->natoms != sys->natoms)
+ {
+ gmx_fatal(FARGS, "number of coordinates in coordinate file (%s, %d)\n"
+ " does not match topology (%s, %d)",
+ confin, state->natoms, topfile, sys->natoms);
+ }
+ else
+ {
+ /* make space for coordinates and velocities */
+ char title[STRLEN];
+ snew(confat, 1);
+ init_t_atoms(confat, state->natoms, FALSE);
+ init_state(state, state->natoms, 0, 0, 0, 0);
+ read_stx_conf(confin, title, confat, state->x, state->v, NULL, state->box);
+ /* This call fixes the box shape for runs with pressure scaling */
+ set_box_rel(ir, state);
+
+ nmismatch = check_atom_names(topfile, confin, sys, confat);
+ free_t_atoms(confat, TRUE);
+ sfree(confat);
+
+ if (nmismatch)
+ {
+ sprintf(buf, "%d non-matching atom name%s\n"
+ "atom names from %s will be used\n"
+ "atom names from %s will be ignored\n",
+ nmismatch, (nmismatch == 1) ? "" : "s", topfile, confin);
+ warning(wi, buf);
+ }
+ if (bVerbose)
+ {
+ fprintf(stderr, "double-checking input for internal consistency...\n");
+ }
+ double_check(ir, state->box, nint_ftype(sys, molinfo, F_CONSTR), wi);
+ }
+
+ if (bGenVel)
+ {
+ real *mass;
+ gmx_mtop_atomloop_all_t aloop;
+ t_atom *atom;
+ unsigned int useed;
+
+ snew(mass, state->natoms);
+ aloop = gmx_mtop_atomloop_all_init(sys);
+ while (gmx_mtop_atomloop_all_next(aloop, &i, &atom))
+ {
+ mass[i] = atom->m;
+ }
+
+ useed = opts->seed;
+ if (opts->seed == -1)
+ {
+ useed = (int)gmx_rng_make_seed();
+ fprintf(stderr, "Setting gen_seed to %u\n", useed);
+ }
+ maxwell_speed(opts->tempi, useed, sys, state->v);
+
+ stop_cm(stdout, state->natoms, mass, state->x, state->v);
+ sfree(mass);
+ }
+
+ *nmi = nrmols;
+ *mi = molinfo;
+}
+
+static void copy_state(const char *slog, t_trxframe *fr,
+ gmx_bool bReadVel, t_state *state,
+ double *use_time)
+{
+ int i;
+
+ if (fr->not_ok & FRAME_NOT_OK)
+ {
+ gmx_fatal(FARGS, "Can not start from an incomplete frame");
+ }
+ if (!fr->bX)
+ {
+ gmx_fatal(FARGS, "Did not find a frame with coordinates in file %s",
+ slog);
+ }
+
+ for (i = 0; i < state->natoms; i++)
+ {
+ copy_rvec(fr->x[i], state->x[i]);
+ }
+ if (bReadVel)
+ {
+ if (!fr->bV)
+ {
+ gmx_incons("Trajecory frame unexpectedly does not contain velocities");
+ }
+ for (i = 0; i < state->natoms; i++)
+ {
+ copy_rvec(fr->v[i], state->v[i]);
+ }
+ }
+ if (fr->bBox)
+ {
+ copy_mat(fr->box, state->box);
+ }
+
+ *use_time = fr->time;
+}
+
+static void cont_status(const char *slog, const char *ener,
+ gmx_bool bNeedVel, gmx_bool bGenVel, real fr_time,
+ t_inputrec *ir, t_state *state,
+ gmx_mtop_t *sys,
+ const output_env_t oenv)
+/* If fr_time == -1 read the last frame available which is complete */
+{
+ gmx_bool bReadVel;
+ t_trxframe fr;
+ t_trxstatus *fp;
+ int i;
+ double use_time;
+
+ bReadVel = (bNeedVel && !bGenVel);
+
+ fprintf(stderr,
+ "Reading Coordinates%s and Box size from old trajectory\n",
+ bReadVel ? ", Velocities" : "");
+ if (fr_time == -1)
+ {
+ fprintf(stderr, "Will read whole trajectory\n");
+ }
+ else
+ {
+ fprintf(stderr, "Will read till time %g\n", fr_time);
+ }
+ if (!bReadVel)
+ {
+ if (bGenVel)
+ {
+ fprintf(stderr, "Velocities generated: "
+ "ignoring velocities in input trajectory\n");
+ }
+ read_first_frame(oenv, &fp, slog, &fr, TRX_NEED_X);
+ }
+ else
+ {
+ read_first_frame(oenv, &fp, slog, &fr, TRX_NEED_X | TRX_NEED_V);
+
+ if (!fr.bV)
+ {
+ fprintf(stderr,
+ "\n"
+ "WARNING: Did not find a frame with velocities in file %s,\n"
+ " all velocities will be set to zero!\n\n", slog);
+ for (i = 0; i < sys->natoms; i++)
+ {
+ clear_rvec(state->v[i]);
+ }
+ close_trj(fp);
+ /* Search for a frame without velocities */
+ bReadVel = FALSE;
+ read_first_frame(oenv, &fp, slog, &fr, TRX_NEED_X);
+ }
+ }
+
+ state->natoms = fr.natoms;
+
+ if (sys->natoms != state->natoms)
+ {
+ gmx_fatal(FARGS, "Number of atoms in Topology "
+ "is not the same as in Trajectory");
+ }
+ copy_state(slog, &fr, bReadVel, state, &use_time);
+
+ /* Find the appropriate frame */
+ while ((fr_time == -1 || fr.time < fr_time) &&
+ read_next_frame(oenv, fp, &fr))
+ {
+ copy_state(slog, &fr, bReadVel, state, &use_time);
+ }
+
+ close_trj(fp);
+
+ /* Set the relative box lengths for preserving the box shape.
+ * Note that this call can lead to differences in the last bit
+ * with respect to using gmx convert-tpr to create a [TT].tpx[tt] file.
+ */
+ set_box_rel(ir, state);
+
+ fprintf(stderr, "Using frame at t = %g ps\n", use_time);
+ fprintf(stderr, "Starting time for run is %g ps\n", ir->init_t);
+
+ if ((ir->epc != epcNO || ir->etc == etcNOSEHOOVER) && ener)
+ {
+ get_enx_state(ener, use_time, &sys->groups, ir, state);
+ preserve_box_shape(ir, state->box_rel, state->boxv);
+ }
+}
+
+static void read_posres(gmx_mtop_t *mtop, t_molinfo *molinfo, gmx_bool bTopB,
+ char *fn,
+ int rc_scaling, int ePBC,
+ rvec com,
+ warninp_t wi)
+{
+ gmx_bool bFirst = TRUE, *hadAtom;
+ rvec *x, *v, *xp;
+ dvec sum;
+ double totmass;
+ t_atoms dumat;
+ matrix box, invbox;
+ int natoms, npbcdim = 0;
+ char warn_buf[STRLEN], title[STRLEN];
+ int a, i, ai, j, k, mb, nat_molb;
+ gmx_molblock_t *molb;
+ t_params *pr, *prfb;
+ t_atom *atom;
+
+ get_stx_coordnum(fn, &natoms);
+ if (natoms != mtop->natoms)
+ {
+ sprintf(warn_buf, "The number of atoms in %s (%d) does not match the number of atoms in the topology (%d). Will assume that the first %d atoms in the topology and %s match.", fn, natoms, mtop->natoms, min(mtop->natoms, natoms), fn);
+ warning(wi, warn_buf);
+ }
+ snew(x, natoms);
+ snew(v, natoms);
+ init_t_atoms(&dumat, natoms, FALSE);
+ read_stx_conf(fn, title, &dumat, x, v, NULL, box);
+
+ npbcdim = ePBC2npbcdim(ePBC);
+ clear_rvec(com);
+ if (rc_scaling != erscNO)
+ {
+ copy_mat(box, invbox);
+ for (j = npbcdim; j < DIM; j++)
+ {
+ clear_rvec(invbox[j]);
+ invbox[j][j] = 1;
+ }
+ m_inv_ur0(invbox, invbox);
+ }
+
+ /* Copy the reference coordinates to mtop */
+ clear_dvec(sum);
+ totmass = 0;
+ a = 0;
+ snew(hadAtom, natoms);
+ for (mb = 0; mb < mtop->nmolblock; mb++)
+ {
+ molb = &mtop->molblock[mb];
+ nat_molb = molb->nmol*mtop->moltype[molb->type].atoms.nr;
+ pr = &(molinfo[molb->type].plist[F_POSRES]);
+ prfb = &(molinfo[molb->type].plist[F_FBPOSRES]);
+ if (pr->nr > 0 || prfb->nr > 0)
+ {
+ atom = mtop->moltype[molb->type].atoms.atom;
+ for (i = 0; (i < pr->nr); i++)
+ {
+ ai = pr->param[i].AI;
+ if (ai >= natoms)
+ {
+ gmx_fatal(FARGS, "Position restraint atom index (%d) in moltype '%s' is larger than number of atoms in %s (%d).\n",
+ ai+1, *molinfo[molb->type].name, fn, natoms);
+ }
+ hadAtom[ai] = TRUE;
+ if (rc_scaling == erscCOM)
+ {
+ /* Determine the center of mass of the posres reference coordinates */
+ for (j = 0; j < npbcdim; j++)
+ {
+ sum[j] += atom[ai].m*x[a+ai][j];
+ }
+ totmass += atom[ai].m;
+ }
+ }
+ /* Same for flat-bottomed posres, but do not count an atom twice for COM */
+ for (i = 0; (i < prfb->nr); i++)
+ {
+ ai = prfb->param[i].AI;
+ if (ai >= natoms)
+ {
+ gmx_fatal(FARGS, "Position restraint atom index (%d) in moltype '%s' is larger than number of atoms in %s (%d).\n",
+ ai+1, *molinfo[molb->type].name, fn, natoms);
+ }
+ if (rc_scaling == erscCOM && hadAtom[ai] == FALSE)
+ {
+ /* Determine the center of mass of the posres reference coordinates */
+ for (j = 0; j < npbcdim; j++)
+ {
+ sum[j] += atom[ai].m*x[a+ai][j];
+ }
+ totmass += atom[ai].m;
+ }
+ }
+ if (!bTopB)
+ {
+ molb->nposres_xA = nat_molb;
+ snew(molb->posres_xA, molb->nposres_xA);
+ for (i = 0; i < nat_molb; i++)
+ {
+ copy_rvec(x[a+i], molb->posres_xA[i]);
+ }
+ }
+ else
+ {
+ molb->nposres_xB = nat_molb;
+ snew(molb->posres_xB, molb->nposres_xB);
+ for (i = 0; i < nat_molb; i++)
+ {
+ copy_rvec(x[a+i], molb->posres_xB[i]);
+ }
+ }
+ }
+ a += nat_molb;
+ }
+ if (rc_scaling == erscCOM)
+ {
+ if (totmass == 0)
+ {
+ gmx_fatal(FARGS, "The total mass of the position restraint atoms is 0");
+ }
+ for (j = 0; j < npbcdim; j++)
+ {
+ com[j] = sum[j]/totmass;
+ }
+ fprintf(stderr, "The center of mass of the position restraint coord's is %6.3f %6.3f %6.3f\n", com[XX], com[YY], com[ZZ]);
+ }
+
+ if (rc_scaling != erscNO)
+ {
+ assert(npbcdim <= DIM);
+
+ for (mb = 0; mb < mtop->nmolblock; mb++)
+ {
+ molb = &mtop->molblock[mb];
+ nat_molb = molb->nmol*mtop->moltype[molb->type].atoms.nr;
+ if (molb->nposres_xA > 0 || molb->nposres_xB > 0)
+ {
+ xp = (!bTopB ? molb->posres_xA : molb->posres_xB);
+ for (i = 0; i < nat_molb; i++)
+ {
+ for (j = 0; j < npbcdim; j++)
+ {
+ if (rc_scaling == erscALL)
+ {
+ /* Convert from Cartesian to crystal coordinates */
+ xp[i][j] *= invbox[j][j];
+ for (k = j+1; k < npbcdim; k++)
+ {
+ xp[i][j] += invbox[k][j]*xp[i][k];
+ }
+ }
+ else if (rc_scaling == erscCOM)
+ {
+ /* Subtract the center of mass */
+ xp[i][j] -= com[j];
+ }
+ }
+ }
+ }
+ }
+
+ if (rc_scaling == erscCOM)
+ {
+ /* Convert the COM from Cartesian to crystal coordinates */
+ for (j = 0; j < npbcdim; j++)
+ {
+ com[j] *= invbox[j][j];
+ for (k = j+1; k < npbcdim; k++)
+ {
+ com[j] += invbox[k][j]*com[k];
+ }
+ }
+ }
+ }
+
+ free_t_atoms(&dumat, TRUE);
+ sfree(x);
+ sfree(v);
+ sfree(hadAtom);
+}
+
+static void gen_posres(gmx_mtop_t *mtop, t_molinfo *mi,
+ char *fnA, char *fnB,
+ int rc_scaling, int ePBC,
+ rvec com, rvec comB,
+ warninp_t wi)
+{
+ int i, j;
+
+ read_posres (mtop, mi, FALSE, fnA, rc_scaling, ePBC, com, wi);
+ if (strcmp(fnA, fnB) != 0)
+ {
+ read_posres(mtop, mi, TRUE, fnB, rc_scaling, ePBC, comB, wi);
+ }
+}
+
+static void set_wall_atomtype(gpp_atomtype_t at, t_gromppopts *opts,
+ t_inputrec *ir, warninp_t wi)
+{
+ int i;
+ char warn_buf[STRLEN];
+
+ if (ir->nwall > 0)
+ {
+ fprintf(stderr, "Searching the wall atom type(s)\n");
+ }
+ for (i = 0; i < ir->nwall; i++)
+ {
+ ir->wall_atomtype[i] = get_atomtype_type(opts->wall_atomtype[i], at);
+ if (ir->wall_atomtype[i] == NOTSET)
+ {
+ sprintf(warn_buf, "Specified wall atom type %s is not defined", opts->wall_atomtype[i]);
+ warning_error(wi, warn_buf);
+ }
+ }
+}
+
+static int nrdf_internal(t_atoms *atoms)
+{
+ int i, nmass, nrdf;
+
+ nmass = 0;
+ for (i = 0; i < atoms->nr; i++)
+ {
+ /* Vsite ptype might not be set here yet, so also check the mass */
+ if ((atoms->atom[i].ptype == eptAtom ||
+ atoms->atom[i].ptype == eptNucleus)
+ && atoms->atom[i].m > 0)
+ {
+ nmass++;
+ }
+ }
+ switch (nmass)
+ {
+ case 0: nrdf = 0; break;
+ case 1: nrdf = 0; break;
+ case 2: nrdf = 1; break;
+ default: nrdf = nmass*3 - 6; break;
+ }
+
+ return nrdf;
+}
+
+void
+spline1d( double dx,
+ double * y,
+ int n,
+ double * u,
+ double * y2 )
+{
+ int i;
+ double p, q;
+
+ y2[0] = 0.0;
+ u[0] = 0.0;
+
+ for (i = 1; i < n-1; i++)
+ {
+ p = 0.5*y2[i-1]+2.0;
+ y2[i] = -0.5/p;
+ q = (y[i+1]-2.0*y[i]+y[i-1])/dx;
+ u[i] = (3.0*q/dx-0.5*u[i-1])/p;
+ }
+
+ y2[n-1] = 0.0;
+
+ for (i = n-2; i >= 0; i--)
+ {
+ y2[i] = y2[i]*y2[i+1]+u[i];
+ }
+}
+
+
+void
+interpolate1d( double xmin,
+ double dx,
+ double * ya,
+ double * y2a,
+ double x,
+ double * y,
+ double * y1)
+{
+ int ix;
+ double a, b;
+
+ ix = (x-xmin)/dx;
+
+ a = (xmin+(ix+1)*dx-x)/dx;
+ b = (x-xmin-ix*dx)/dx;
+
+ *y = a*ya[ix]+b*ya[ix+1]+((a*a*a-a)*y2a[ix]+(b*b*b-b)*y2a[ix+1])*(dx*dx)/6.0;
+ *y1 = (ya[ix+1]-ya[ix])/dx-(3.0*a*a-1.0)/6.0*dx*y2a[ix]+(3.0*b*b-1.0)/6.0*dx*y2a[ix+1];
+}
+
+
+void
+setup_cmap (int grid_spacing,
+ int nc,
+ real * grid,
+ gmx_cmap_t * cmap_grid)
+{
+ double *tmp_u, *tmp_u2, *tmp_yy, *tmp_y1, *tmp_t2, *tmp_grid;
+
+ int i, j, k, ii, jj, kk, idx;
+ int offset;
+ double dx, xmin, v, v1, v2, v12;
+ double phi, psi;
+
+ snew(tmp_u, 2*grid_spacing);
+ snew(tmp_u2, 2*grid_spacing);
+ snew(tmp_yy, 2*grid_spacing);
+ snew(tmp_y1, 2*grid_spacing);
+ snew(tmp_t2, 2*grid_spacing*2*grid_spacing);
+ snew(tmp_grid, 2*grid_spacing*2*grid_spacing);
+
+ dx = 360.0/grid_spacing;
+ xmin = -180.0-dx*grid_spacing/2;
+
+ for (kk = 0; kk < nc; kk++)
+ {
+ /* Compute an offset depending on which cmap we are using
+ * Offset will be the map number multiplied with the
+ * grid_spacing * grid_spacing * 2
+ */
+ offset = kk * grid_spacing * grid_spacing * 2;
+
+ for (i = 0; i < 2*grid_spacing; i++)
+ {
+ ii = (i+grid_spacing-grid_spacing/2)%grid_spacing;
+
+ for (j = 0; j < 2*grid_spacing; j++)
+ {
+ jj = (j+grid_spacing-grid_spacing/2)%grid_spacing;
+ tmp_grid[i*grid_spacing*2+j] = grid[offset+ii*grid_spacing+jj];
+ }
+ }
+
+ for (i = 0; i < 2*grid_spacing; i++)
+ {
+ spline1d(dx, &(tmp_grid[2*grid_spacing*i]), 2*grid_spacing, tmp_u, &(tmp_t2[2*grid_spacing*i]));
+ }
+
+ for (i = grid_spacing/2; i < grid_spacing+grid_spacing/2; i++)
+ {
+ ii = i-grid_spacing/2;
+ phi = ii*dx-180.0;
+
+ for (j = grid_spacing/2; j < grid_spacing+grid_spacing/2; j++)
+ {
+ jj = j-grid_spacing/2;
+ psi = jj*dx-180.0;
+
+ for (k = 0; k < 2*grid_spacing; k++)
+ {
+ interpolate1d(xmin, dx, &(tmp_grid[2*grid_spacing*k]),
+ &(tmp_t2[2*grid_spacing*k]), psi, &tmp_yy[k], &tmp_y1[k]);
+ }
+
+ spline1d(dx, tmp_yy, 2*grid_spacing, tmp_u, tmp_u2);
+ interpolate1d(xmin, dx, tmp_yy, tmp_u2, phi, &v, &v1);
+ spline1d(dx, tmp_y1, 2*grid_spacing, tmp_u, tmp_u2);
+ interpolate1d(xmin, dx, tmp_y1, tmp_u2, phi, &v2, &v12);
+
+ idx = ii*grid_spacing+jj;
+ cmap_grid->cmapdata[kk].cmap[idx*4] = grid[offset+ii*grid_spacing+jj];
+ cmap_grid->cmapdata[kk].cmap[idx*4+1] = v1;
+ cmap_grid->cmapdata[kk].cmap[idx*4+2] = v2;
+ cmap_grid->cmapdata[kk].cmap[idx*4+3] = v12;
+ }
+ }
+ }
+}
+
+void init_cmap_grid(gmx_cmap_t *cmap_grid, int ngrid, int grid_spacing)
+{
+ int i, k, nelem;
+
+ cmap_grid->ngrid = ngrid;
+ cmap_grid->grid_spacing = grid_spacing;
+ nelem = cmap_grid->grid_spacing*cmap_grid->grid_spacing;
+
+ snew(cmap_grid->cmapdata, ngrid);
+
+ for (i = 0; i < cmap_grid->ngrid; i++)
+ {
+ snew(cmap_grid->cmapdata[i].cmap, 4*nelem);
+ }
+}
+
+
+static int count_constraints(gmx_mtop_t *mtop, t_molinfo *mi, warninp_t wi)
+{
+ int count, count_mol, i, mb;
+ gmx_molblock_t *molb;
+ t_params *plist;
+ char buf[STRLEN];
+
+ count = 0;
+ for (mb = 0; mb < mtop->nmolblock; mb++)
+ {
+ count_mol = 0;
+ molb = &mtop->molblock[mb];
+ plist = mi[molb->type].plist;
+
+ for (i = 0; i < F_NRE; i++)
+ {
+ if (i == F_SETTLE)
+ {
+ count_mol += 3*plist[i].nr;
+ }
+ else if (interaction_function[i].flags & IF_CONSTRAINT)
+ {
+ count_mol += plist[i].nr;
+ }
+ }
+
+ if (count_mol > nrdf_internal(&mi[molb->type].atoms))
+ {
+ sprintf(buf,
+ "Molecule type '%s' has %d constraints.\n"
+ "For stability and efficiency there should not be more constraints than internal number of degrees of freedom: %d.\n",
+ *mi[molb->type].name, count_mol,
+ nrdf_internal(&mi[molb->type].atoms));
+ warning(wi, buf);
+ }
+ count += molb->nmol*count_mol;
+ }
+
+ return count;
+}
+
+static void check_gbsa_params_charged(gmx_mtop_t *sys, gpp_atomtype_t atype)
+{
+ int i, nmiss, natoms, mt;
+ real q;
+ const t_atoms *atoms;
+
+ nmiss = 0;
+ for (mt = 0; mt < sys->nmoltype; mt++)
+ {
+ atoms = &sys->moltype[mt].atoms;
+ natoms = atoms->nr;
+
+ for (i = 0; i < natoms; i++)
+ {
+ q = atoms->atom[i].q;
+ if ((get_atomtype_radius(atoms->atom[i].type, atype) == 0 ||
+ get_atomtype_vol(atoms->atom[i].type, atype) == 0 ||
+ get_atomtype_surftens(atoms->atom[i].type, atype) == 0 ||
+ get_atomtype_gb_radius(atoms->atom[i].type, atype) == 0 ||
+ get_atomtype_S_hct(atoms->atom[i].type, atype) == 0) &&
+ q != 0)
+ {
+ fprintf(stderr, "\nGB parameter(s) zero for atom type '%s' while charge is %g\n",
+ get_atomtype_name(atoms->atom[i].type, atype), q);
+ nmiss++;
+ }
+ }
+ }
+
+ if (nmiss > 0)
+ {
+ gmx_fatal(FARGS, "Can't do GB electrostatics; the implicit_genborn_params section of the forcefield has parameters with value zero for %d atomtypes that occur as charged atoms.", nmiss);
+ }
+}
+
+
+static void check_gbsa_params(gpp_atomtype_t atype)
+{
+ int nmiss, i;
+
+ /* If we are doing GBSA, check that we got the parameters we need
+ * This checking is to see if there are GBSA paratmeters for all
+ * atoms in the force field. To go around this for testing purposes
+ * comment out the nerror++ counter temporarily
+ */
+ nmiss = 0;
+ for (i = 0; i < get_atomtype_ntypes(atype); i++)
+ {
+ if (get_atomtype_radius(i, atype) < 0 ||
+ get_atomtype_vol(i, atype) < 0 ||
+ get_atomtype_surftens(i, atype) < 0 ||
+ get_atomtype_gb_radius(i, atype) < 0 ||
+ get_atomtype_S_hct(i, atype) < 0)
+ {
+ fprintf(stderr, "\nGB parameter(s) missing or negative for atom type '%s'\n",
+ get_atomtype_name(i, atype));
+ nmiss++;
+ }
+ }
+
+ if (nmiss > 0)
+ {
+ gmx_fatal(FARGS, "Can't do GB electrostatics; the implicit_genborn_params section of the forcefield is missing parameters for %d atomtypes or they might be negative.", nmiss);
+ }
+
+}
+
+static real calc_temp(const gmx_mtop_t *mtop,
+ const t_inputrec *ir,
+ rvec *v)
+{
+ double sum_mv2;
+ gmx_mtop_atomloop_all_t aloop;
+ t_atom *atom;
+ int a;
+ int nrdf, g;
+
+ sum_mv2 = 0;
+
+ aloop = gmx_mtop_atomloop_all_init(mtop);
+ while (gmx_mtop_atomloop_all_next(aloop, &a, &atom))
+ {
+ sum_mv2 += atom->m*norm2(v[a]);
+ }
+
+ nrdf = 0;
+ for (g = 0; g < ir->opts.ngtc; g++)
+ {
+ nrdf += ir->opts.nrdf[g];
+ }
+
+ return sum_mv2/(nrdf*BOLTZ);
+}
+
+static real get_max_reference_temp(const t_inputrec *ir,
+ warninp_t wi)
+{
+ real ref_t;
+ int i;
+ gmx_bool bNoCoupl;
+
+ ref_t = 0;
+ bNoCoupl = FALSE;
+ for (i = 0; i < ir->opts.ngtc; i++)
+ {
+ if (ir->opts.tau_t[i] < 0)
+ {
+ bNoCoupl = TRUE;
+ }
+ else
+ {
+ ref_t = max(ref_t, ir->opts.ref_t[i]);
+ }
+ }
+
+ if (bNoCoupl)
+ {
+ char buf[STRLEN];
+
+ sprintf(buf, "Some temperature coupling groups do not use temperature coupling. We will assume their temperature is not more than %.3f K. If their temperature is higher, the energy error and the Verlet buffer might be underestimated.",
+ ref_t);
+ warning(wi, buf);
+ }
+
+ return ref_t;
+}
+
+static void set_verlet_buffer(const gmx_mtop_t *mtop,
+ t_inputrec *ir,
+ real buffer_temp,
+ matrix box,
+ warninp_t wi)
+{
+ int i;
+ verletbuf_list_setup_t ls;
+ real rlist_1x1;
+ int n_nonlin_vsite;
+ char warn_buf[STRLEN];
+
+ printf("Determining Verlet buffer for a tolerance of %g kJ/mol/ps at %g K\n", ir->verletbuf_tol, buffer_temp);
+
+ /* Calculate the buffer size for simple atom vs atoms list */
+ ls.cluster_size_i = 1;
+ ls.cluster_size_j = 1;
+ calc_verlet_buffer_size(mtop, det(box), ir, buffer_temp,
+ &ls, &n_nonlin_vsite, &rlist_1x1);
+
+ /* Set the pair-list buffer size in ir */
+ verletbuf_get_list_setup(FALSE, &ls);
+ calc_verlet_buffer_size(mtop, det(box), ir, buffer_temp,
+ &ls, &n_nonlin_vsite, &ir->rlist);
+
+ if (n_nonlin_vsite > 0)
+ {
+ sprintf(warn_buf, "There are %d non-linear virtual site constructions. Their contribution to the energy error is approximated. In most cases this does not affect the error significantly.", n_nonlin_vsite);
+ warning_note(wi, warn_buf);
+ }
+
+ printf("Calculated rlist for %dx%d atom pair-list as %.3f nm, buffer size %.3f nm\n",
+ 1, 1, rlist_1x1, rlist_1x1-max(ir->rvdw, ir->rcoulomb));
+
+ ir->rlistlong = ir->rlist;
+ printf("Set rlist, assuming %dx%d atom pair-list, to %.3f nm, buffer size %.3f nm\n",
+ ls.cluster_size_i, ls.cluster_size_j,
+ ir->rlist, ir->rlist-max(ir->rvdw, ir->rcoulomb));
+
+ if (sqr(ir->rlistlong) >= max_cutoff2(ir->ePBC, box))
+ {
+ gmx_fatal(FARGS, "The pair-list cut-off (%g nm) is longer than half the shortest box vector or longer than the smallest box diagonal element (%g nm). Increase the box size or decrease nstlist or increase verlet-buffer-tolerance.", ir->rlistlong, sqrt(max_cutoff2(ir->ePBC, box)));
+ }
+}
+
+int gmx_grompp(int argc, char *argv[])
+{
+ static const char *desc[] = {
+ "[THISMODULE] (the gromacs preprocessor)",
+ "reads a molecular topology file, checks the validity of the",
+ "file, expands the topology from a molecular description to an atomic",
+ "description. The topology file contains information about",
+ "molecule types and the number of molecules, the preprocessor",
+ "copies each molecule as needed. ",
+ "There is no limitation on the number of molecule types. ",
+ "Bonds and bond-angles can be converted into constraints, separately",
+ "for hydrogens and heavy atoms.",
+ "Then a coordinate file is read and velocities can be generated",
+ "from a Maxwellian distribution if requested.",
+ "[THISMODULE] also reads parameters for [gmx-mdrun] ",
+ "(eg. number of MD steps, time step, cut-off), and others such as",
+ "NEMD parameters, which are corrected so that the net acceleration",
+ "is zero.",
+ "Eventually a binary file is produced that can serve as the sole input",
+ "file for the MD program.[PAR]",
+
+ "[THISMODULE] uses the atom names from the topology file. The atom names",
+ "in the coordinate file (option [TT]-c[tt]) are only read to generate",
+ "warnings when they do not match the atom names in the topology.",
+ "Note that the atom names are irrelevant for the simulation as",
+ "only the atom types are used for generating interaction parameters.[PAR]",
+
+ "[THISMODULE] uses a built-in preprocessor to resolve includes, macros, ",
+ "etc. The preprocessor supports the following keywords:[PAR]",
+ "#ifdef VARIABLE[BR]",
+ "#ifndef VARIABLE[BR]",
+ "#else[BR]",
+ "#endif[BR]",
+ "#define VARIABLE[BR]",
+ "#undef VARIABLE[BR]"
+ "#include \"filename\"[BR]",
+ "#include <filename>[PAR]",
+ "The functioning of these statements in your topology may be modulated by",
+ "using the following two flags in your [TT].mdp[tt] file:[PAR]",
+ "[TT]define = -DVARIABLE1 -DVARIABLE2[BR]",
+ "include = -I/home/john/doe[tt][BR]",
+ "For further information a C-programming textbook may help you out.",
+ "Specifying the [TT]-pp[tt] flag will get the pre-processed",
+ "topology file written out so that you can verify its contents.[PAR]",
+
+ /* cpp has been unnecessary for some time, hasn't it?
+ "If your system does not have a C-preprocessor, you can still",
+ "use [TT]grompp[tt], but you do not have access to the features ",
+ "from the cpp. Command line options to the C-preprocessor can be given",
+ "in the [TT].mdp[tt] file. See your local manual (man cpp).[PAR]",
+ */
+
+ "When using position restraints a file with restraint coordinates",
+ "can be supplied with [TT]-r[tt], otherwise restraining will be done",
+ "with respect to the conformation from the [TT]-c[tt] option.",
+ "For free energy calculation the the coordinates for the B topology",
+ "can be supplied with [TT]-rb[tt], otherwise they will be equal to",
+ "those of the A topology.[PAR]",
+
+ "Starting coordinates can be read from trajectory with [TT]-t[tt].",
+ "The last frame with coordinates and velocities will be read,",
+ "unless the [TT]-time[tt] option is used. Only if this information",
+ "is absent will the coordinates in the [TT]-c[tt] file be used.",
+ "Note that these velocities will not be used when [TT]gen_vel = yes[tt]",
+ "in your [TT].mdp[tt] file. An energy file can be supplied with",
+ "[TT]-e[tt] to read Nose-Hoover and/or Parrinello-Rahman coupling",
+ "variables.[PAR]",
+
+ "[THISMODULE] can be used to restart simulations (preserving",
+ "continuity) by supplying just a checkpoint file with [TT]-t[tt].",
+ "However, for simply changing the number of run steps to extend",
+ "a run, using [gmx-convert-tpr] is more convenient than [THISMODULE].",
+ "You then supply the old checkpoint file directly to [gmx-mdrun]",
+ "with [TT]-cpi[tt]. If you wish to change the ensemble or things",
+ "like output frequency, then supplying the checkpoint file to",
+ "[THISMODULE] with [TT]-t[tt] along with a new [TT].mdp[tt] file",
+ "with [TT]-f[tt] is the recommended procedure.[PAR]",
+
+ "By default, all bonded interactions which have constant energy due to",
+ "virtual site constructions will be removed. If this constant energy is",
+ "not zero, this will result in a shift in the total energy. All bonded",
+ "interactions can be kept by turning off [TT]-rmvsbds[tt]. Additionally,",
+ "all constraints for distances which will be constant anyway because",
+ "of virtual site constructions will be removed. If any constraints remain",
+ "which involve virtual sites, a fatal error will result.[PAR]"
+
+ "To verify your run input file, please take note of all warnings",
+ "on the screen, and correct where necessary. Do also look at the contents",
+ "of the [TT]mdout.mdp[tt] file; this contains comment lines, as well as",
+ "the input that [THISMODULE] has read. If in doubt, you can start [THISMODULE]",
+ "with the [TT]-debug[tt] option which will give you more information",
+ "in a file called [TT]grompp.log[tt] (along with real debug info). You",
+ "can see the contents of the run input file with the [gmx-dump]",
+ "program. [gmx-check] can be used to compare the contents of two",
+ "run input files.[PAR]"
+
+ "The [TT]-maxwarn[tt] option can be used to override warnings printed",
+ "by [THISMODULE] that otherwise halt output. In some cases, warnings are",
+ "harmless, but usually they are not. The user is advised to carefully",
+ "interpret the output messages before attempting to bypass them with",
+ "this option."
+ };
+ t_gromppopts *opts;
+ gmx_mtop_t *sys;
+ int nmi;
+ t_molinfo *mi;
+ gpp_atomtype_t atype;
+ t_inputrec *ir;
+ int natoms, nvsite, comb, mt;
+ t_params *plist;
+ t_state state;
+ matrix box;
+ real max_spacing, fudgeQQ;
+ double reppow;
+ char fn[STRLEN], fnB[STRLEN];
+ const char *mdparin;
+ int ntype;
+ gmx_bool bNeedVel, bGenVel;
+ gmx_bool have_atomnumber;
+ int n12, n13, n14;
+ t_params *gb_plist = NULL;
+ gmx_genborn_t *born = NULL;
+ output_env_t oenv;
+ gmx_bool bVerbose = FALSE;
+ warninp_t wi;
+ char warn_buf[STRLEN];
+ unsigned int useed;
+ t_atoms IMDatoms; /* Atoms to be operated on interactively (IMD) */
+
+ t_filenm fnm[] = {
+ { efMDP, NULL, NULL, ffREAD },
+ { efMDP, "-po", "mdout", ffWRITE },
+ { efSTX, "-c", NULL, ffREAD },
+ { efSTX, "-r", NULL, ffOPTRD },
+ { efSTX, "-rb", NULL, ffOPTRD },
+ { efNDX, NULL, NULL, ffOPTRD },
+ { efTOP, NULL, NULL, ffREAD },
+ { efTOP, "-pp", "processed", ffOPTWR },
+ { efTPX, "-o", NULL, ffWRITE },
+ { efTRN, "-t", NULL, ffOPTRD },
+ { efEDR, "-e", NULL, ffOPTRD },
+ /* This group is needed by the VMD viewer as the start configuration for IMD sessions: */
+ { efGRO, "-imd", "imdgroup", ffOPTWR },
+ { efTRN, "-ref", "rotref", ffOPTRW }
+ };
+#define NFILE asize(fnm)
+
+ /* Command line options */
+ static gmx_bool bRenum = TRUE;
+ static gmx_bool bRmVSBds = TRUE, bZero = FALSE;
+ static int i, maxwarn = 0;
+ static real fr_time = -1;
+ t_pargs pa[] = {
+ { "-v", FALSE, etBOOL, {&bVerbose},
+ "Be loud and noisy" },
+ { "-time", FALSE, etREAL, {&fr_time},
+ "Take frame at or first after this time." },
+ { "-rmvsbds", FALSE, etBOOL, {&bRmVSBds},
+ "Remove constant bonded interactions with virtual sites" },
+ { "-maxwarn", FALSE, etINT, {&maxwarn},
+ "Number of allowed warnings during input processing. Not for normal use and may generate unstable systems" },
+ { "-zero", FALSE, etBOOL, {&bZero},
+ "Set parameters for bonded interactions without defaults to zero instead of generating an error" },
+ { "-renum", FALSE, etBOOL, {&bRenum},
+ "Renumber atomtypes and minimize number of atomtypes" }
+ };
+
+ /* Initiate some variables */
+ snew(ir, 1);
+ snew(opts, 1);
+ init_ir(ir, opts);
+
+ /* Parse the command line */
+ if (!parse_common_args(&argc, argv, 0, NFILE, fnm, asize(pa), pa,
+ asize(desc), desc, 0, NULL, &oenv))
+ {
+ return 0;
+ }
+
+ wi = init_warning(TRUE, maxwarn);
+
+ /* PARAMETER file processing */
+ mdparin = opt2fn("-f", NFILE, fnm);
+ set_warning_line(wi, mdparin, -1);
+ get_ir(mdparin, opt2fn("-po", NFILE, fnm), ir, opts, wi);
+
+ if (bVerbose)
+ {
+ fprintf(stderr, "checking input for internal consistency...\n");
+ }
+ check_ir(mdparin, ir, opts, wi);
+
+ if (ir->ld_seed == -1)
+ {
+ ir->ld_seed = (gmx_int64_t)gmx_rng_make_seed();
+ fprintf(stderr, "Setting the LD random seed to %"GMX_PRId64 "\n", ir->ld_seed);
+ }
+
+ if (ir->expandedvals->lmc_seed == -1)
+ {
+ ir->expandedvals->lmc_seed = (int)gmx_rng_make_seed();
+ fprintf(stderr, "Setting the lambda MC random seed to %d\n", ir->expandedvals->lmc_seed);
+ }
+
+ bNeedVel = EI_STATE_VELOCITY(ir->eI);
+ bGenVel = (bNeedVel && opts->bGenVel);
+ if (bGenVel && ir->bContinuation)
+ {
+ sprintf(warn_buf,
+ "Generating velocities is inconsistent with attempting "
+ "to continue a previous run. Choose only one of "
+ "gen-vel = yes and continuation = yes.");
+ warning_error(wi, warn_buf);
+ }
+
+ snew(plist, F_NRE);
+ init_plist(plist);
+ snew(sys, 1);
+ atype = init_atomtype();
+ if (debug)
+ {
+ pr_symtab(debug, 0, "Just opened", &sys->symtab);
+ }
+
+ strcpy(fn, ftp2fn(efTOP, NFILE, fnm));
+ if (!gmx_fexist(fn))
+ {
+ gmx_fatal(FARGS, "%s does not exist", fn);
+ }
+ new_status(fn, opt2fn_null("-pp", NFILE, fnm), opt2fn("-c", NFILE, fnm),
+ opts, ir, bZero, bGenVel, bVerbose, &state,
+ atype, sys, &nmi, &mi, plist, &comb, &reppow, &fudgeQQ,
+ opts->bMorse,
+ wi);
+
+ if (debug)
+ {
+ pr_symtab(debug, 0, "After new_status", &sys->symtab);
+ }
+
+ nvsite = 0;
+ /* set parameters for virtual site construction (not for vsiten) */
+ for (mt = 0; mt < sys->nmoltype; mt++)
+ {
+ nvsite +=
+ set_vsites(bVerbose, &sys->moltype[mt].atoms, atype, mi[mt].plist);
+ }
+ /* now throw away all obsolete bonds, angles and dihedrals: */
+ /* note: constraints are ALWAYS removed */
+ if (nvsite)
+ {
+ for (mt = 0; mt < sys->nmoltype; mt++)
+ {
+ clean_vsite_bondeds(mi[mt].plist, sys->moltype[mt].atoms.nr, bRmVSBds);
+ }
+ }
+
++ if (nvsite && ir->eI == eiNM)
++ {
++ gmx_fatal(FARGS, "Normal Mode analysis is not supported with virtual sites.\nIf you'd like to help with adding support, we have an open discussion at http://redmine.gromacs.org/issues/879\n");
++ }
++
+ if (ir->cutoff_scheme == ecutsVERLET)
+ {
+ fprintf(stderr, "Removing all charge groups because cutoff-scheme=%s\n",
+ ecutscheme_names[ir->cutoff_scheme]);
+
+ /* Remove all charge groups */
+ gmx_mtop_remove_chargegroups(sys);
+ }
+
+ if (count_constraints(sys, mi, wi) && (ir->eConstrAlg == econtSHAKE))
+ {
+ if (ir->eI == eiCG || ir->eI == eiLBFGS)
+ {
+ sprintf(warn_buf, "Can not do %s with %s, use %s",
+ EI(ir->eI), econstr_names[econtSHAKE], econstr_names[econtLINCS]);
+ warning_error(wi, warn_buf);
+ }
+ if (ir->bPeriodicMols)
+ {
+ sprintf(warn_buf, "Can not do periodic molecules with %s, use %s",
+ econstr_names[econtSHAKE], econstr_names[econtLINCS]);
+ warning_error(wi, warn_buf);
+ }
+ }
+
+ if (EI_SD (ir->eI) && ir->etc != etcNO)
+ {
+ warning_note(wi, "Temperature coupling is ignored with SD integrators.");
+ }
+
+ /* If we are doing QM/MM, check that we got the atom numbers */
+ have_atomnumber = TRUE;
+ for (i = 0; i < get_atomtype_ntypes(atype); i++)
+ {
+ have_atomnumber = have_atomnumber && (get_atomtype_atomnumber(i, atype) >= 0);
+ }
+ if (!have_atomnumber && ir->bQMMM)
+ {
+ warning_error(wi,
+ "\n"
+ "It appears as if you are trying to run a QM/MM calculation, but the force\n"
+ "field you are using does not contain atom numbers fields. This is an\n"
+ "optional field (introduced in Gromacs 3.3) for general runs, but mandatory\n"
+ "for QM/MM. The good news is that it is easy to add - put the atom number as\n"
+ "an integer just before the mass column in ffXXXnb.itp.\n"
+ "NB: United atoms have the same atom numbers as normal ones.\n\n");
+ }
+
+ if (ir->bAdress)
+ {
+ if ((ir->adress->const_wf > 1) || (ir->adress->const_wf < 0))
+ {
+ warning_error(wi, "AdResS contant weighting function should be between 0 and 1\n\n");
+ }
+ /** TODO check size of ex+hy width against box size */
+ }
+
+ /* Check for errors in the input now, since they might cause problems
+ * during processing further down.
+ */
+ check_warning_error(wi, FARGS);
+
+ if (opt2bSet("-r", NFILE, fnm))
+ {
+ sprintf(fn, "%s", opt2fn("-r", NFILE, fnm));
+ }
+ else
+ {
+ sprintf(fn, "%s", opt2fn("-c", NFILE, fnm));
+ }
+ if (opt2bSet("-rb", NFILE, fnm))
+ {
+ sprintf(fnB, "%s", opt2fn("-rb", NFILE, fnm));
+ }
+ else
+ {
+ strcpy(fnB, fn);
+ }
+
+ if (nint_ftype(sys, mi, F_POSRES) > 0 || nint_ftype(sys, mi, F_FBPOSRES) > 0)
+ {
+ if (bVerbose)
+ {
+ fprintf(stderr, "Reading position restraint coords from %s", fn);
+ if (strcmp(fn, fnB) == 0)
+ {
+ fprintf(stderr, "\n");
+ }
+ else
+ {
+ fprintf(stderr, " and %s\n", fnB);
+ }
+ }
+ gen_posres(sys, mi, fn, fnB,
+ ir->refcoord_scaling, ir->ePBC,
+ ir->posres_com, ir->posres_comB,
+ wi);
+ }
+
+ /* If we are using CMAP, setup the pre-interpolation grid */
+ if (plist->ncmap > 0)
+ {
+ init_cmap_grid(&sys->ffparams.cmap_grid, plist->nc, plist->grid_spacing);
+ setup_cmap(plist->grid_spacing, plist->nc, plist->cmap, &sys->ffparams.cmap_grid);
+ }
+
+ set_wall_atomtype(atype, opts, ir, wi);
+ if (bRenum)
+ {
+ renum_atype(plist, sys, ir->wall_atomtype, atype, bVerbose);
+ ntype = get_atomtype_ntypes(atype);
+ }
+
+ if (ir->implicit_solvent != eisNO)
+ {
+ /* Now we have renumbered the atom types, we can check the GBSA params */
+ check_gbsa_params(atype);
+
+ /* Check that all atoms that have charge and/or LJ-parameters also have
+ * sensible GB-parameters
+ */
+ check_gbsa_params_charged(sys, atype);
+ }
+
+ /* PELA: Copy the atomtype data to the topology atomtype list */
+ copy_atomtype_atomtypes(atype, &(sys->atomtypes));
+
+ if (debug)
+ {
+ pr_symtab(debug, 0, "After renum_atype", &sys->symtab);
+ }
+
+ if (bVerbose)
+ {
+ fprintf(stderr, "converting bonded parameters...\n");
+ }
+
+ ntype = get_atomtype_ntypes(atype);
+ convert_params(ntype, plist, mi, comb, reppow, fudgeQQ, sys);
+
+ if (debug)
+ {
+ pr_symtab(debug, 0, "After convert_params", &sys->symtab);
+ }
+
+ /* set ptype to VSite for virtual sites */
+ for (mt = 0; mt < sys->nmoltype; mt++)
+ {
+ set_vsites_ptype(FALSE, &sys->moltype[mt]);
+ }
+ if (debug)
+ {
+ pr_symtab(debug, 0, "After virtual sites", &sys->symtab);
+ }
+ /* Check velocity for virtual sites and shells */
+ if (bGenVel)
+ {
+ check_vel(sys, state.v);
+ }
+
+ /* check masses */
+ check_mol(sys, wi);
+
+ for (i = 0; i < sys->nmoltype; i++)
+ {
+ check_cg_sizes(ftp2fn(efTOP, NFILE, fnm), &sys->moltype[i].cgs, wi);
+ }
+
+ if (EI_DYNAMICS(ir->eI) && ir->eI != eiBD)
+ {
+ check_bonds_timestep(sys, ir->delta_t, wi);
+ }
+
+ if (EI_ENERGY_MINIMIZATION(ir->eI) && 0 == ir->nsteps)
+ {
+ warning_note(wi, "Zero-step energy minimization will alter the coordinates before calculating the energy. If you just want the energy of a single point, try zero-step MD (with unconstrained_start = yes). To do multiple single-point energy evaluations of different configurations of the same topology, use mdrun -rerun.");
+ }
+
+ check_warning_error(wi, FARGS);
+
+ if (bVerbose)
+ {
+ fprintf(stderr, "initialising group options...\n");
+ }
+ do_index(mdparin, ftp2fn_null(efNDX, NFILE, fnm),
+ sys, bVerbose, ir,
+ bGenVel ? state.v : NULL,
+ wi);
+
+ if (ir->cutoff_scheme == ecutsVERLET && ir->verletbuf_tol > 0 &&
+ ir->nstlist > 1)
+ {
+ if (EI_DYNAMICS(ir->eI) && inputrec2nboundeddim(ir) == 3)
+ {
+ real buffer_temp;
+
+ if (EI_MD(ir->eI) && ir->etc == etcNO)
+ {
+ if (bGenVel)
+ {
+ buffer_temp = opts->tempi;
+ }
+ else
+ {
+ buffer_temp = calc_temp(sys, ir, state.v);
+ }
+ if (buffer_temp > 0)
+ {
+ sprintf(warn_buf, "NVE simulation: will use the initial temperature of %.3f K for determining the Verlet buffer size", buffer_temp);
+ warning_note(wi, warn_buf);
+ }
+ else
+ {
+ sprintf(warn_buf, "NVE simulation with an initial temperature of zero: will use a Verlet buffer of %d%%. Check your energy drift!",
+ (int)(verlet_buffer_ratio_NVE_T0*100 + 0.5));
+ warning_note(wi, warn_buf);
+ }
+ }
+ else
+ {
+ buffer_temp = get_max_reference_temp(ir, wi);
+ }
+
+ if (EI_MD(ir->eI) && ir->etc == etcNO && buffer_temp == 0)
+ {
+ /* NVE with initial T=0: we add a fixed ratio to rlist.
+ * Since we don't actually use verletbuf_tol, we set it to -1
+ * so it can't be misused later.
+ */
+ ir->rlist *= 1.0 + verlet_buffer_ratio_NVE_T0;
+ ir->verletbuf_tol = -1;
+ }
+ else
+ {
+ /* We warn for NVE simulations with >1(.1)% drift tolerance */
+ const real drift_tol = 0.01;
+ real ener_runtime;
+
+ /* We use 2 DOF per atom = 2kT pot+kin energy, to be on
+ * the safe side with constraints (without constraints: 3 DOF).
+ */
+ ener_runtime = 2*BOLTZ*buffer_temp/(ir->nsteps*ir->delta_t);
+
+ if (EI_MD(ir->eI) && ir->etc == etcNO && ir->nstlist > 1 &&
+ ir->nsteps > 0 &&
+ ir->verletbuf_tol > 1.1*drift_tol*ener_runtime)
+ {
+ sprintf(warn_buf, "You are using a Verlet buffer tolerance of %g kJ/mol/ps for an NVE simulation of length %g ps, which can give a final drift of %d%%. For conserving energy to %d%%, you might need to set verlet-buffer-tolerance to %.1e.",
+ ir->verletbuf_tol, ir->nsteps*ir->delta_t,
+ (int)(ir->verletbuf_tol/ener_runtime*100 + 0.5),
+ (int)(100*drift_tol + 0.5),
+ drift_tol*ener_runtime);
+ warning_note(wi, warn_buf);
+ }
+
+ set_verlet_buffer(sys, ir, buffer_temp, state.box, wi);
+ }
+ }
+ }
+
+ /* Init the temperature coupling state */
+ init_gtc_state(&state, ir->opts.ngtc, 0, ir->opts.nhchainlength); /* need to add nnhpres here? */
+
+ if (bVerbose)
+ {
+ fprintf(stderr, "Checking consistency between energy and charge groups...\n");
+ }
+ check_eg_vs_cg(sys);
+
+ if (debug)
+ {
+ pr_symtab(debug, 0, "After index", &sys->symtab);
+ }
+
+ triple_check(mdparin, ir, sys, wi);
+ close_symtab(&sys->symtab);
+ if (debug)
+ {
+ pr_symtab(debug, 0, "After close", &sys->symtab);
+ }
+
+ /* make exclusions between QM atoms */
+ if (ir->bQMMM)
+ {
+ if (ir->QMMMscheme == eQMMMschemenormal && ir->ns_type == ensSIMPLE)
+ {
+ gmx_fatal(FARGS, "electrostatic embedding only works with grid neighboursearching, use ns-type=grid instead\n");
+ }
+ else
+ {
+ generate_qmexcl(sys, ir, wi);
+ }
+ }
+
+ if (ftp2bSet(efTRN, NFILE, fnm))
+ {
+ if (bVerbose)
+ {
+ fprintf(stderr, "getting data from old trajectory ...\n");
+ }
+ cont_status(ftp2fn(efTRN, NFILE, fnm), ftp2fn_null(efEDR, NFILE, fnm),
+ bNeedVel, bGenVel, fr_time, ir, &state, sys, oenv);
+ }
+
+ if (ir->ePBC == epbcXY && ir->nwall != 2)
+ {
+ clear_rvec(state.box[ZZ]);
+ }
+
+ if (ir->cutoff_scheme != ecutsVERLET && ir->rlist > 0)
+ {
+ set_warning_line(wi, mdparin, -1);
+ check_chargegroup_radii(sys, ir, state.x, wi);
+ }
+
+ if (EEL_FULL(ir->coulombtype) || EVDW_PME(ir->vdwtype))
+ {
+ /* Calculate the optimal grid dimensions */
+ copy_mat(state.box, box);
+ if (ir->ePBC == epbcXY && ir->nwall == 2)
+ {
+ svmul(ir->wall_ewald_zfac, box[ZZ], box[ZZ]);
+ }
+ if (ir->nkx > 0 && ir->nky > 0 && ir->nkz > 0)
+ {
+ /* Mark fourier_spacing as not used */
+ ir->fourier_spacing = 0;
+ }
+ else if (ir->nkx != 0 && ir->nky != 0 && ir->nkz != 0)
+ {
+ set_warning_line(wi, mdparin, -1);
+ warning_error(wi, "Some of the Fourier grid sizes are set, but all of them need to be set.");
+ }
+ max_spacing = calc_grid(stdout, box, ir->fourier_spacing,
+ &(ir->nkx), &(ir->nky), &(ir->nkz));
+ }
+
+ /* MRS: eventually figure out better logic for initializing the fep
+ values that makes declaring the lambda and declaring the state not
+ potentially conflict if not handled correctly. */
+ if (ir->efep != efepNO)
+ {
+ state.fep_state = ir->fepvals->init_fep_state;
+ for (i = 0; i < efptNR; i++)
+ {
+ /* init_lambda trumps state definitions*/
+ if (ir->fepvals->init_lambda >= 0)
+ {
+ state.lambda[i] = ir->fepvals->init_lambda;
+ }
+ else
+ {
+ if (ir->fepvals->all_lambda[i] == NULL)
+ {
+ gmx_fatal(FARGS, "Values of lambda not set for a free energy calculation!");
+ }
+ else
+ {
+ state.lambda[i] = ir->fepvals->all_lambda[i][state.fep_state];
+ }
+ }
+ }
+ }
+
+ if (ir->ePull != epullNO)
+ {
+ set_pull_init(ir, sys, state.x, state.box, state.lambda[efptMASS], oenv, opts->pull_start);
+ }
+
+ if (ir->bRot)
+ {
+ set_reference_positions(ir->rot, state.x, state.box,
+ opt2fn("-ref", NFILE, fnm), opt2bSet("-ref", NFILE, fnm),
+ wi);
+ }
+
+ /* reset_multinr(sys); */
+
+ if (EEL_PME(ir->coulombtype))
+ {
+ float ratio = pme_load_estimate(sys, ir, state.box);
+ fprintf(stderr, "Estimate for the relative computational load of the PME mesh part: %.2f\n", ratio);
+ /* With free energy we might need to do PME both for the A and B state
+ * charges. This will double the cost, but the optimal performance will
+ * then probably be at a slightly larger cut-off and grid spacing.
+ */
+ if ((ir->efep == efepNO && ratio > 1.0/2.0) ||
+ (ir->efep != efepNO && ratio > 2.0/3.0))
+ {
+ warning_note(wi,
+ "The optimal PME mesh load for parallel simulations is below 0.5\n"
+ "and for highly parallel simulations between 0.25 and 0.33,\n"
+ "for higher performance, increase the cut-off and the PME grid spacing.\n");
+ if (ir->efep != efepNO)
+ {
+ warning_note(wi,
+ "For free energy simulations, the optimal load limit increases from 0.5 to 0.667\n");
+ }
+ }
+ }
+
+ {
+ char warn_buf[STRLEN];
+ double cio = compute_io(ir, sys->natoms, &sys->groups, F_NRE, 1);
+ sprintf(warn_buf, "This run will generate roughly %.0f Mb of data", cio);
+ if (cio > 2000)
+ {
+ set_warning_line(wi, mdparin, -1);
+ warning_note(wi, warn_buf);
+ }
+ else
+ {
+ printf("%s\n", warn_buf);
+ }
+ }
+
+ if (bVerbose)
+ {
+ fprintf(stderr, "writing run input file...\n");
+ }
+
+ done_warning(wi, FARGS);
+ write_tpx_state(ftp2fn(efTPX, NFILE, fnm), ir, &state, sys);
+
+ /* Output IMD group, if bIMD is TRUE */
+ write_IMDgroup_to_file(ir->bIMD, ir, &state, sys, NFILE, fnm);
+
+ done_atomtype(atype);
+ done_mtop(sys, TRUE);
+ done_inputrec_strings();
+
+ return 0;
+}
--- /dev/null
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
+ * Copyright (c) 2001-2004, The GROMACS development team.
+ * Copyright (c) 2013,2014, by the GROMACS development team, led by
+ * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+ * and including many others, as listed in the AUTHORS file in the
+ * top-level source directory and at http://www.gromacs.org.
+ *
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
+ * of the License, or (at your option) any later version.
+ *
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+ *
+ * If you want to redistribute modifications to GROMACS, please
+ * consider that scientific software is very special. Version
+ * control is crucial - bugs must be traceable. We will be happy to
+ * consider code for inclusion in the official distribution, but
+ * derived work must not be called official GROMACS. Details are found
+ * in the README & COPYING files - if they are missing, get the
+ * official version at http://www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the research papers on the package. Check out http://www.gromacs.org.
+ */
+#ifdef HAVE_CONFIG_H
+#include <config.h>
+#endif
+
+#include <ctype.h>
+#include <stdlib.h>
+#include <limits.h>
+#include "sysstuff.h"
+#include "gromacs/utility/smalloc.h"
+#include "typedefs.h"
+#include "physics.h"
+#include "names.h"
+#include "gmx_fatal.h"
+#include "macros.h"
+#include "index.h"
+#include "symtab.h"
+#include "gromacs/utility/cstringutil.h"
+#include "readinp.h"
+#include "warninp.h"
+#include "readir.h"
+#include "toputil.h"
+#include "index.h"
+#include "network.h"
+#include "vec.h"
+#include "pbc.h"
+#include "mtop_util.h"
+#include "chargegroup.h"
+#include "inputrec.h"
+#include "calc_verletbuf.h"
+
+#define MAXPTR 254
+#define NOGID 255
+
+/* Resource parameters
+ * Do not change any of these until you read the instruction
+ * in readinp.h. Some cpp's do not take spaces after the backslash
+ * (like the c-shell), which will give you a very weird compiler
+ * message.
+ */
+
+typedef struct t_inputrec_strings
+{
+ char tcgrps[STRLEN], tau_t[STRLEN], ref_t[STRLEN],
+ acc[STRLEN], accgrps[STRLEN], freeze[STRLEN], frdim[STRLEN],
+ energy[STRLEN], user1[STRLEN], user2[STRLEN], vcm[STRLEN], x_compressed_groups[STRLEN],
+ couple_moltype[STRLEN], orirefitgrp[STRLEN], egptable[STRLEN], egpexcl[STRLEN],
+ wall_atomtype[STRLEN], wall_density[STRLEN], deform[STRLEN], QMMM[STRLEN],
+ imd_grp[STRLEN];
+ char fep_lambda[efptNR][STRLEN];
+ char lambda_weights[STRLEN];
+ char **pull_grp;
+ char **rot_grp;
+ char anneal[STRLEN], anneal_npoints[STRLEN],
+ anneal_time[STRLEN], anneal_temp[STRLEN];
+ char QMmethod[STRLEN], QMbasis[STRLEN], QMcharge[STRLEN], QMmult[STRLEN],
+ bSH[STRLEN], CASorbitals[STRLEN], CASelectrons[STRLEN], SAon[STRLEN],
+ SAoff[STRLEN], SAsteps[STRLEN], bTS[STRLEN], bOPT[STRLEN];
+ char efield_x[STRLEN], efield_xt[STRLEN], efield_y[STRLEN],
+ efield_yt[STRLEN], efield_z[STRLEN], efield_zt[STRLEN];
+
+} gmx_inputrec_strings;
+
+static gmx_inputrec_strings *is = NULL;
+
+void init_inputrec_strings()
+{
+ if (is)
+ {
+ gmx_incons("Attempted to call init_inputrec_strings before calling done_inputrec_strings. Only one inputrec (i.e. .mdp file) can be parsed at a time.");
+ }
+ snew(is, 1);
+}
+
+void done_inputrec_strings()
+{
+ sfree(is);
+ is = NULL;
+}
+
+static char swapgrp[STRLEN], splitgrp0[STRLEN], splitgrp1[STRLEN], solgrp[STRLEN];
+
+enum {
+ egrptpALL, /* All particles have to be a member of a group. */
+ egrptpALL_GENREST, /* A rest group with name is generated for particles *
+ * that are not part of any group. */
+ egrptpPART, /* As egrptpALL_GENREST, but no name is generated *
+ * for the rest group. */
+ egrptpONE /* Merge all selected groups into one group, *
+ * make a rest group for the remaining particles. */
+};
+
+static const char *constraints[eshNR+1] = {
+ "none", "h-bonds", "all-bonds", "h-angles", "all-angles", NULL
+};
+
+static const char *couple_lam[ecouplamNR+1] = {
+ "vdw-q", "vdw", "q", "none", NULL
+};
+
+void init_ir(t_inputrec *ir, t_gromppopts *opts)
+{
+ snew(opts->include, STRLEN);
+ snew(opts->define, STRLEN);
+ snew(ir->fepvals, 1);
+ snew(ir->expandedvals, 1);
+ snew(ir->simtempvals, 1);
+}
+
+static void GetSimTemps(int ntemps, t_simtemp *simtemp, double *temperature_lambdas)
+{
+
+ int i;
+
+ for (i = 0; i < ntemps; i++)
+ {
+ /* simple linear scaling -- allows more control */
+ if (simtemp->eSimTempScale == esimtempLINEAR)
+ {
+ simtemp->temperatures[i] = simtemp->simtemp_low + (simtemp->simtemp_high-simtemp->simtemp_low)*temperature_lambdas[i];
+ }
+ else if (simtemp->eSimTempScale == esimtempGEOMETRIC) /* should give roughly equal acceptance for constant heat capacity . . . */
+ {
+ simtemp->temperatures[i] = simtemp->simtemp_low * pow(simtemp->simtemp_high/simtemp->simtemp_low, (1.0*i)/(ntemps-1));
+ }
+ else if (simtemp->eSimTempScale == esimtempEXPONENTIAL)
+ {
+ simtemp->temperatures[i] = simtemp->simtemp_low + (simtemp->simtemp_high-simtemp->simtemp_low)*((exp(temperature_lambdas[i])-1)/(exp(1.0)-1));
+ }
+ else
+ {
+ char errorstr[128];
+ sprintf(errorstr, "eSimTempScale=%d not defined", simtemp->eSimTempScale);
+ gmx_fatal(FARGS, errorstr);
+ }
+ }
+}
+
+
+
+static void _low_check(gmx_bool b, char *s, warninp_t wi)
+{
+ if (b)
+ {
+ warning_error(wi, s);
+ }
+}
+
+static void check_nst(const char *desc_nst, int nst,
+ const char *desc_p, int *p,
+ warninp_t wi)
+{
+ char buf[STRLEN];
+
+ if (*p > 0 && *p % nst != 0)
+ {
+ /* Round up to the next multiple of nst */
+ *p = ((*p)/nst + 1)*nst;
+ sprintf(buf, "%s should be a multiple of %s, changing %s to %d\n",
+ desc_p, desc_nst, desc_p, *p);
+ warning(wi, buf);
+ }
+}
+
+static gmx_bool ir_NVE(const t_inputrec *ir)
+{
+ return ((ir->eI == eiMD || EI_VV(ir->eI)) && ir->etc == etcNO);
+}
+
+static int lcd(int n1, int n2)
+{
+ int d, i;
+
+ d = 1;
+ for (i = 2; (i <= n1 && i <= n2); i++)
+ {
+ if (n1 % i == 0 && n2 % i == 0)
+ {
+ d = i;
+ }
+ }
+
+ return d;
+}
+
+static void process_interaction_modifier(const t_inputrec *ir, int *eintmod)
+{
+ if (*eintmod == eintmodPOTSHIFT_VERLET)
+ {
+ if (ir->cutoff_scheme == ecutsVERLET)
+ {
+ *eintmod = eintmodPOTSHIFT;
+ }
+ else
+ {
+ *eintmod = eintmodNONE;
+ }
+ }
+}
+
+void check_ir(const char *mdparin, t_inputrec *ir, t_gromppopts *opts,
+ warninp_t wi)
+/* Check internal consistency.
+ * NOTE: index groups are not set here yet, don't check things
+ * like temperature coupling group options here, but in triple_check
+ */
+{
+ /* Strange macro: first one fills the err_buf, and then one can check
+ * the condition, which will print the message and increase the error
+ * counter.
+ */
+#define CHECK(b) _low_check(b, err_buf, wi)
+ char err_buf[256], warn_buf[STRLEN];
+ int i, j;
+ int ns_type = 0;
+ real dt_coupl = 0;
+ real dt_pcoupl;
+ int nstcmin;
+ t_lambda *fep = ir->fepvals;
+ t_expanded *expand = ir->expandedvals;
+
+ set_warning_line(wi, mdparin, -1);
+
+ /* BASIC CUT-OFF STUFF */
+ if (ir->rcoulomb < 0)
+ {
+ warning_error(wi, "rcoulomb should be >= 0");
+ }
+ if (ir->rvdw < 0)
+ {
+ warning_error(wi, "rvdw should be >= 0");
+ }
+ if (ir->rlist < 0 &&
+ !(ir->cutoff_scheme == ecutsVERLET && ir->verletbuf_tol > 0))
+ {
+ warning_error(wi, "rlist should be >= 0");
+ }
+
+ process_interaction_modifier(ir, &ir->coulomb_modifier);
+ process_interaction_modifier(ir, &ir->vdw_modifier);
+
+ if (ir->cutoff_scheme == ecutsGROUP)
+ {
+ warning_note(wi,
+ "The group cutoff scheme is deprecated in Gromacs 5.0 and will be removed in a future "
+ "release when all interaction forms are supported for the verlet scheme. The verlet "
+ "scheme already scales better, and it is compatible with GPUs and other accelerators.");
+
+ /* BASIC CUT-OFF STUFF */
+ if (ir->rlist == 0 ||
+ !((ir_coulomb_might_be_zero_at_cutoff(ir) && ir->rcoulomb > ir->rlist) ||
+ (ir_vdw_might_be_zero_at_cutoff(ir) && ir->rvdw > ir->rlist)))
+ {
+ /* No switched potential and/or no twin-range:
+ * we can set the long-range cut-off to the maximum of the other cut-offs.
+ */
+ ir->rlistlong = max_cutoff(ir->rlist, max_cutoff(ir->rvdw, ir->rcoulomb));
+ }
+ else if (ir->rlistlong < 0)
+ {
+ ir->rlistlong = max_cutoff(ir->rlist, max_cutoff(ir->rvdw, ir->rcoulomb));
+ sprintf(warn_buf, "rlistlong was not set, setting it to %g (no buffer)",
+ ir->rlistlong);
+ warning(wi, warn_buf);
+ }
+ if (ir->rlistlong == 0 && ir->ePBC != epbcNONE)
+ {
+ warning_error(wi, "Can not have an infinite cut-off with PBC");
+ }
+ if (ir->rlistlong > 0 && (ir->rlist == 0 || ir->rlistlong < ir->rlist))
+ {
+ warning_error(wi, "rlistlong can not be shorter than rlist");
+ }
+ if (IR_TWINRANGE(*ir) && ir->nstlist <= 0)
+ {
+ warning_error(wi, "Can not have nstlist<=0 with twin-range interactions");
+ }
+ }
+
+ if (ir->rlistlong == ir->rlist)
+ {
+ ir->nstcalclr = 0;
+ }
+ else if (ir->rlistlong > ir->rlist && ir->nstcalclr == 0)
+ {
+ warning_error(wi, "With different cutoffs for electrostatics and VdW, nstcalclr must be -1 or a positive number");
+ }
+
+ if (ir->cutoff_scheme == ecutsVERLET)
+ {
+ real rc_max;
+
+ /* Normal Verlet type neighbor-list, currently only limited feature support */
+ if (inputrec2nboundeddim(ir) < 3)
+ {
+ warning_error(wi, "With Verlet lists only full pbc or pbc=xy with walls is supported");
+ }
+ if (ir->rcoulomb != ir->rvdw)
+ {
+ warning_error(wi, "With Verlet lists rcoulomb!=rvdw is not supported");
+ }
+ if (ir->vdwtype == evdwSHIFT || ir->vdwtype == evdwSWITCH)
+ {
+ if (ir->vdw_modifier == eintmodNONE ||
+ ir->vdw_modifier == eintmodPOTSHIFT)
+ {
+ ir->vdw_modifier = (ir->vdwtype == evdwSHIFT ? eintmodFORCESWITCH : eintmodPOTSWITCH);
+
+ sprintf(warn_buf, "Replacing vdwtype=%s by the equivalent combination of vdwtype=%s and vdw_modifier=%s", evdw_names[ir->vdwtype], evdw_names[evdwCUT], eintmod_names[ir->vdw_modifier]);
+ warning_note(wi, warn_buf);
+
+ ir->vdwtype = evdwCUT;
+ }
+ else
+ {
+ sprintf(warn_buf, "Unsupported combination of vdwtype=%s and vdw_modifier=%s", evdw_names[ir->vdwtype], eintmod_names[ir->vdw_modifier]);
+ warning_error(wi, warn_buf);
+ }
+ }
+
+ if (!(ir->vdwtype == evdwCUT || ir->vdwtype == evdwPME))
+ {
+ warning_error(wi, "With Verlet lists only cut-off and PME LJ interactions are supported");
+ }
+ if (!(ir->coulombtype == eelCUT ||
+ (EEL_RF(ir->coulombtype) && ir->coulombtype != eelRF_NEC) ||
+ EEL_PME(ir->coulombtype) || ir->coulombtype == eelEWALD))
+ {
+ warning_error(wi, "With Verlet lists only cut-off, reaction-field, PME and Ewald electrostatics are supported");
+ }
+ if (!(ir->coulomb_modifier == eintmodNONE ||
+ ir->coulomb_modifier == eintmodPOTSHIFT))
+ {
+ sprintf(warn_buf, "coulomb_modifier=%s is not supported with the Verlet cut-off scheme", eintmod_names[ir->coulomb_modifier]);
+ warning_error(wi, warn_buf);
+ }
+
+ if (ir->nstlist <= 0)
+ {
+ warning_error(wi, "With Verlet lists nstlist should be larger than 0");
+ }
+
+ if (ir->nstlist < 10)
+ {
+ warning_note(wi, "With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation.");
+ }
+
+ rc_max = max(ir->rvdw, ir->rcoulomb);
+
+ if (ir->verletbuf_tol <= 0)
+ {
+ if (ir->verletbuf_tol == 0)
+ {
+ warning_error(wi, "Can not have Verlet buffer tolerance of exactly 0");
+ }
+
+ if (ir->rlist < rc_max)
+ {
+ warning_error(wi, "With verlet lists rlist can not be smaller than rvdw or rcoulomb");
+ }
+
+ if (ir->rlist == rc_max && ir->nstlist > 1)
+ {
+ warning_note(wi, "rlist is equal to rvdw and/or rcoulomb: there is no explicit Verlet buffer. The cluster pair list does have a buffering effect, but choosing a larger rlist might be necessary for good energy conservation.");
+ }
+ }
+ else
+ {
+ if (ir->rlist > rc_max)
+ {
+ warning_note(wi, "You have set rlist larger than the interaction cut-off, but you also have verlet-buffer-tolerance > 0. Will set rlist using verlet-buffer-tolerance.");
+ }
+
+ if (ir->nstlist == 1)
+ {
+ /* No buffer required */
+ ir->rlist = rc_max;
+ }
+ else
+ {
+ if (EI_DYNAMICS(ir->eI))
+ {
+ if (inputrec2nboundeddim(ir) < 3)
+ {
+ warning_error(wi, "The box volume is required for calculating rlist from the energy drift with verlet-buffer-tolerance > 0. You are using at least one unbounded dimension, so no volume can be computed. Either use a finite box, or set rlist yourself together with verlet-buffer-tolerance = -1.");
+ }
+ /* Set rlist temporarily so we can continue processing */
+ ir->rlist = rc_max;
+ }
+ else
+ {
+ /* Set the buffer to 5% of the cut-off */
+ ir->rlist = (1.0 + verlet_buffer_ratio_nodynamics)*rc_max;
+ }
+ }
+ }
+
+ /* No twin-range calculations with Verlet lists */
+ ir->rlistlong = ir->rlist;
+ }
+
+ if (ir->nstcalclr == -1)
+ {
+ /* if rlist=rlistlong, this will later be changed to nstcalclr=0 */
+ ir->nstcalclr = ir->nstlist;
+ }
+ else if (ir->nstcalclr > 0)
+ {
+ if (ir->nstlist > 0 && (ir->nstlist % ir->nstcalclr != 0))
+ {
+ warning_error(wi, "nstlist must be evenly divisible by nstcalclr. Use nstcalclr = -1 to automatically follow nstlist");
+ }
+ }
+ else if (ir->nstcalclr < -1)
+ {
+ warning_error(wi, "nstcalclr must be a positive number (divisor of nstcalclr), or -1 to follow nstlist.");
+ }
+
+ if (EEL_PME(ir->coulombtype) && ir->rcoulomb > ir->rvdw && ir->nstcalclr > 1)
+ {
+ warning_error(wi, "When used with PME, the long-range component of twin-range interactions must be updated every step (nstcalclr)");
+ }
+
+ /* GENERAL INTEGRATOR STUFF */
+ if (!(ir->eI == eiMD || EI_VV(ir->eI)))
+ {
+ ir->etc = etcNO;
+ }
+ if (ir->eI == eiVVAK)
+ {
+ sprintf(warn_buf, "Integrator method %s is implemented primarily for validation purposes; for molecular dynamics, you should probably be using %s or %s", ei_names[eiVVAK], ei_names[eiMD], ei_names[eiVV]);
+ warning_note(wi, warn_buf);
+ }
+ if (!EI_DYNAMICS(ir->eI))
+ {
+ ir->epc = epcNO;
+ }
+ if (EI_DYNAMICS(ir->eI))
+ {
+ if (ir->nstcalcenergy < 0)
+ {
+ ir->nstcalcenergy = ir_optimal_nstcalcenergy(ir);
+ if (ir->nstenergy != 0 && ir->nstenergy < ir->nstcalcenergy)
+ {
+ /* nstcalcenergy larger than nstener does not make sense.
+ * We ideally want nstcalcenergy=nstener.
+ */
+ if (ir->nstlist > 0)
+ {
+ ir->nstcalcenergy = lcd(ir->nstenergy, ir->nstlist);
+ }
+ else
+ {
+ ir->nstcalcenergy = ir->nstenergy;
+ }
+ }
+ }
+ else if ( (ir->nstenergy > 0 && ir->nstcalcenergy > ir->nstenergy) ||
+ (ir->efep != efepNO && ir->fepvals->nstdhdl > 0 &&
+ (ir->nstcalcenergy > ir->fepvals->nstdhdl) ) )
+
+ {
+ const char *nsten = "nstenergy";
+ const char *nstdh = "nstdhdl";
+ const char *min_name = nsten;
+ int min_nst = ir->nstenergy;
+
+ /* find the smallest of ( nstenergy, nstdhdl ) */
+ if (ir->efep != efepNO && ir->fepvals->nstdhdl > 0 &&
+ (ir->nstenergy == 0 || ir->fepvals->nstdhdl < ir->nstenergy))
+ {
+ min_nst = ir->fepvals->nstdhdl;
+ min_name = nstdh;
+ }
+ /* If the user sets nstenergy small, we should respect that */
+ sprintf(warn_buf,
+ "Setting nstcalcenergy (%d) equal to %s (%d)",
+ ir->nstcalcenergy, min_name, min_nst);
+ warning_note(wi, warn_buf);
+ ir->nstcalcenergy = min_nst;
+ }
+
+ if (ir->epc != epcNO)
+ {
+ if (ir->nstpcouple < 0)
+ {
+ ir->nstpcouple = ir_optimal_nstpcouple(ir);
+ }
+ }
+ if (IR_TWINRANGE(*ir))
+ {
+ check_nst("nstlist", ir->nstlist,
+ "nstcalcenergy", &ir->nstcalcenergy, wi);
+ if (ir->epc != epcNO)
+ {
+ check_nst("nstlist", ir->nstlist,
+ "nstpcouple", &ir->nstpcouple, wi);
+ }
+ }
+
+ if (ir->nstcalcenergy > 0)
+ {
+ if (ir->efep != efepNO)
+ {
+ /* nstdhdl should be a multiple of nstcalcenergy */
+ check_nst("nstcalcenergy", ir->nstcalcenergy,
+ "nstdhdl", &ir->fepvals->nstdhdl, wi);
+ /* nstexpanded should be a multiple of nstcalcenergy */
+ check_nst("nstcalcenergy", ir->nstcalcenergy,
+ "nstexpanded", &ir->expandedvals->nstexpanded, wi);
+ }
+ /* for storing exact averages nstenergy should be
+ * a multiple of nstcalcenergy
+ */
+ check_nst("nstcalcenergy", ir->nstcalcenergy,
+ "nstenergy", &ir->nstenergy, wi);
+ }
+ }
+
+ /* LD STUFF */
+ if ((EI_SD(ir->eI) || ir->eI == eiBD) &&
+ ir->bContinuation && ir->ld_seed != -1)
+ {
+ warning_note(wi, "You are doing a continuation with SD or BD, make sure that ld_seed is different from the previous run (using ld_seed=-1 will ensure this)");
+ }
+
+ /* TPI STUFF */
+ if (EI_TPI(ir->eI))
+ {
+ sprintf(err_buf, "TPI only works with pbc = %s", epbc_names[epbcXYZ]);
+ CHECK(ir->ePBC != epbcXYZ);
+ sprintf(err_buf, "TPI only works with ns = %s", ens_names[ensGRID]);
+ CHECK(ir->ns_type != ensGRID);
+ sprintf(err_buf, "with TPI nstlist should be larger than zero");
+ CHECK(ir->nstlist <= 0);
+ sprintf(err_buf, "TPI does not work with full electrostatics other than PME");
+ CHECK(EEL_FULL(ir->coulombtype) && !EEL_PME(ir->coulombtype));
+ }
+
+ /* SHAKE / LINCS */
+ if ( (opts->nshake > 0) && (opts->bMorse) )
+ {
+ sprintf(warn_buf,
+ "Using morse bond-potentials while constraining bonds is useless");
+ warning(wi, warn_buf);
+ }
+
+ if ((EI_SD(ir->eI) || ir->eI == eiBD) &&
+ ir->bContinuation && ir->ld_seed != -1)
+ {
+ warning_note(wi, "You are doing a continuation with SD or BD, make sure that ld_seed is different from the previous run (using ld_seed=-1 will ensure this)");
+ }
+ /* verify simulated tempering options */
+
+ if (ir->bSimTemp)
+ {
+ gmx_bool bAllTempZero = TRUE;
+ for (i = 0; i < fep->n_lambda; i++)
+ {
+ sprintf(err_buf, "Entry %d for %s must be between 0 and 1, instead is %g", i, efpt_names[efptTEMPERATURE], fep->all_lambda[efptTEMPERATURE][i]);
+ CHECK((fep->all_lambda[efptTEMPERATURE][i] < 0) || (fep->all_lambda[efptTEMPERATURE][i] > 1));
+ if (fep->all_lambda[efptTEMPERATURE][i] > 0)
+ {
+ bAllTempZero = FALSE;
+ }
+ }
+ sprintf(err_buf, "if simulated tempering is on, temperature-lambdas may not be all zero");
+ CHECK(bAllTempZero == TRUE);
+
+ sprintf(err_buf, "Simulated tempering is currently only compatible with md-vv");
+ CHECK(ir->eI != eiVV);
+
+ /* check compatability of the temperature coupling with simulated tempering */
+
+ if (ir->etc == etcNOSEHOOVER)
+ {
+ sprintf(warn_buf, "Nose-Hoover based temperature control such as [%s] my not be entirelyconsistent with simulated tempering", etcoupl_names[ir->etc]);
+ warning_note(wi, warn_buf);
+ }
+
+ /* check that the temperatures make sense */
+
+ sprintf(err_buf, "Higher simulated tempering temperature (%g) must be >= than the simulated tempering lower temperature (%g)", ir->simtempvals->simtemp_high, ir->simtempvals->simtemp_low);
+ CHECK(ir->simtempvals->simtemp_high <= ir->simtempvals->simtemp_low);
+
+ sprintf(err_buf, "Higher simulated tempering temperature (%g) must be >= zero", ir->simtempvals->simtemp_high);
+ CHECK(ir->simtempvals->simtemp_high <= 0);
+
+ sprintf(err_buf, "Lower simulated tempering temperature (%g) must be >= zero", ir->simtempvals->simtemp_low);
+ CHECK(ir->simtempvals->simtemp_low <= 0);
+ }
+
+ /* verify free energy options */
+
+ if (ir->efep != efepNO)
+ {
+ fep = ir->fepvals;
+ sprintf(err_buf, "The soft-core power is %d and can only be 1 or 2",
+ fep->sc_power);
+ CHECK(fep->sc_alpha != 0 && fep->sc_power != 1 && fep->sc_power != 2);
+
+ sprintf(err_buf, "The soft-core sc-r-power is %d and can only be 6 or 48",
+ (int)fep->sc_r_power);
+ CHECK(fep->sc_alpha != 0 && fep->sc_r_power != 6.0 && fep->sc_r_power != 48.0);
+
+ sprintf(err_buf, "Can't use postive delta-lambda (%g) if initial state/lambda does not start at zero", fep->delta_lambda);
+ CHECK(fep->delta_lambda > 0 && ((fep->init_fep_state > 0) || (fep->init_lambda > 0)));
+
+ sprintf(err_buf, "Can't use postive delta-lambda (%g) with expanded ensemble simulations", fep->delta_lambda);
+ CHECK(fep->delta_lambda > 0 && (ir->efep == efepEXPANDED));
+
+ sprintf(err_buf, "Can only use expanded ensemble with md-vv for now; should be supported for other integrators in 5.0");
+ CHECK(!(EI_VV(ir->eI)) && (ir->efep == efepEXPANDED));
+
+ sprintf(err_buf, "Free-energy not implemented for Ewald");
+ CHECK(ir->coulombtype == eelEWALD);
+
+ /* check validty of lambda inputs */
+ if (fep->n_lambda == 0)
+ {
+ /* Clear output in case of no states:*/
+ sprintf(err_buf, "init-lambda-state set to %d: no lambda states are defined.", fep->init_fep_state);
+ CHECK((fep->init_fep_state >= 0) && (fep->n_lambda == 0));
+ }
+ else
+ {
+ sprintf(err_buf, "initial thermodynamic state %d does not exist, only goes to %d", fep->init_fep_state, fep->n_lambda-1);
+ CHECK((fep->init_fep_state >= fep->n_lambda));
+ }
+
+ sprintf(err_buf, "Lambda state must be set, either with init-lambda-state or with init-lambda");
+ CHECK((fep->init_fep_state < 0) && (fep->init_lambda < 0));
+
+ sprintf(err_buf, "init-lambda=%g while init-lambda-state=%d. Lambda state must be set either with init-lambda-state or with init-lambda, but not both",
+ fep->init_lambda, fep->init_fep_state);
+ CHECK((fep->init_fep_state >= 0) && (fep->init_lambda >= 0));
+
+
+
+ if ((fep->init_lambda >= 0) && (fep->delta_lambda == 0))
+ {
+ int n_lambda_terms;
+ n_lambda_terms = 0;
+ for (i = 0; i < efptNR; i++)
+ {
+ if (fep->separate_dvdl[i])
+ {
+ n_lambda_terms++;
+ }
+ }
+ if (n_lambda_terms > 1)
+ {
+ sprintf(warn_buf, "If lambda vector states (fep-lambdas, coul-lambdas etc.) are set, don't use init-lambda to set lambda state (except for slow growth). Use init-lambda-state instead.");
+ warning(wi, warn_buf);
+ }
+
+ if (n_lambda_terms < 2 && fep->n_lambda > 0)
+ {
+ warning_note(wi,
+ "init-lambda is deprecated for setting lambda state (except for slow growth). Use init-lambda-state instead.");
+ }
+ }
+
+ for (j = 0; j < efptNR; j++)
+ {
+ for (i = 0; i < fep->n_lambda; i++)
+ {
+ sprintf(err_buf, "Entry %d for %s must be between 0 and 1, instead is %g", i, efpt_names[j], fep->all_lambda[j][i]);
+ CHECK((fep->all_lambda[j][i] < 0) || (fep->all_lambda[j][i] > 1));
+ }
+ }
+
+ if ((fep->sc_alpha > 0) && (!fep->bScCoul))
+ {
+ for (i = 0; i < fep->n_lambda; i++)
+ {
+ sprintf(err_buf, "For state %d, vdw-lambdas (%f) is changing with vdw softcore, while coul-lambdas (%f) is nonzero without coulomb softcore: this will lead to crashes, and is not supported.", i, fep->all_lambda[efptVDW][i],
+ fep->all_lambda[efptCOUL][i]);
+ CHECK((fep->sc_alpha > 0) &&
+ (((fep->all_lambda[efptCOUL][i] > 0.0) &&
+ (fep->all_lambda[efptCOUL][i] < 1.0)) &&
+ ((fep->all_lambda[efptVDW][i] > 0.0) &&
+ (fep->all_lambda[efptVDW][i] < 1.0))));
+ }
+ }
+
+ if ((fep->bScCoul) && (EEL_PME(ir->coulombtype)))
+ {
+ real sigma, lambda, r_sc;
+
+ sigma = 0.34;
+ /* Maximum estimate for A and B charges equal with lambda power 1 */
+ lambda = 0.5;
+ r_sc = pow(lambda*fep->sc_alpha*pow(sigma/ir->rcoulomb, fep->sc_r_power) + 1.0, 1.0/fep->sc_r_power);
+ sprintf(warn_buf, "With PME there is a minor soft core effect present at the cut-off, proportional to (LJsigma/rcoulomb)^%g. This could have a minor effect on energy conservation, but usually other effects dominate. With a common sigma value of %g nm the fraction of the particle-particle potential at the cut-off at lambda=%g is around %.1e, while ewald-rtol is %.1e.",
+ fep->sc_r_power,
+ sigma, lambda, r_sc - 1.0, ir->ewald_rtol);
+ warning_note(wi, warn_buf);
+ }
+
+ /* Free Energy Checks -- In an ideal world, slow growth and FEP would
+ be treated differently, but that's the next step */
+
+ for (i = 0; i < efptNR; i++)
+ {
+ for (j = 0; j < fep->n_lambda; j++)
+ {
+ sprintf(err_buf, "%s[%d] must be between 0 and 1", efpt_names[i], j);
+ CHECK((fep->all_lambda[i][j] < 0) || (fep->all_lambda[i][j] > 1));
+ }
+ }
+ }
+
+ if ((ir->bSimTemp) || (ir->efep == efepEXPANDED))
+ {
+ fep = ir->fepvals;
+ expand = ir->expandedvals;
+
+ /* checking equilibration of weights inputs for validity */
+
+ sprintf(err_buf, "weight-equil-number-all-lambda (%d) is ignored if lmc-weights-equil is not equal to %s",
+ expand->equil_n_at_lam, elmceq_names[elmceqNUMATLAM]);
+ CHECK((expand->equil_n_at_lam > 0) && (expand->elmceq != elmceqNUMATLAM));
+
+ sprintf(err_buf, "weight-equil-number-samples (%d) is ignored if lmc-weights-equil is not equal to %s",
+ expand->equil_samples, elmceq_names[elmceqSAMPLES]);
+ CHECK((expand->equil_samples > 0) && (expand->elmceq != elmceqSAMPLES));
+
+ sprintf(err_buf, "weight-equil-number-steps (%d) is ignored if lmc-weights-equil is not equal to %s",
+ expand->equil_steps, elmceq_names[elmceqSTEPS]);
+ CHECK((expand->equil_steps > 0) && (expand->elmceq != elmceqSTEPS));
+
+ sprintf(err_buf, "weight-equil-wl-delta (%d) is ignored if lmc-weights-equil is not equal to %s",
+ expand->equil_samples, elmceq_names[elmceqWLDELTA]);
+ CHECK((expand->equil_wl_delta > 0) && (expand->elmceq != elmceqWLDELTA));
+
+ sprintf(err_buf, "weight-equil-count-ratio (%f) is ignored if lmc-weights-equil is not equal to %s",
+ expand->equil_ratio, elmceq_names[elmceqRATIO]);
+ CHECK((expand->equil_ratio > 0) && (expand->elmceq != elmceqRATIO));
+
+ sprintf(err_buf, "weight-equil-number-all-lambda (%d) must be a positive integer if lmc-weights-equil=%s",
+ expand->equil_n_at_lam, elmceq_names[elmceqNUMATLAM]);
+ CHECK((expand->equil_n_at_lam <= 0) && (expand->elmceq == elmceqNUMATLAM));
+
+ sprintf(err_buf, "weight-equil-number-samples (%d) must be a positive integer if lmc-weights-equil=%s",
+ expand->equil_samples, elmceq_names[elmceqSAMPLES]);
+ CHECK((expand->equil_samples <= 0) && (expand->elmceq == elmceqSAMPLES));
+
+ sprintf(err_buf, "weight-equil-number-steps (%d) must be a positive integer if lmc-weights-equil=%s",
+ expand->equil_steps, elmceq_names[elmceqSTEPS]);
+ CHECK((expand->equil_steps <= 0) && (expand->elmceq == elmceqSTEPS));
+
+ sprintf(err_buf, "weight-equil-wl-delta (%f) must be > 0 if lmc-weights-equil=%s",
+ expand->equil_wl_delta, elmceq_names[elmceqWLDELTA]);
+ CHECK((expand->equil_wl_delta <= 0) && (expand->elmceq == elmceqWLDELTA));
+
+ sprintf(err_buf, "weight-equil-count-ratio (%f) must be > 0 if lmc-weights-equil=%s",
+ expand->equil_ratio, elmceq_names[elmceqRATIO]);
+ CHECK((expand->equil_ratio <= 0) && (expand->elmceq == elmceqRATIO));
+
+ sprintf(err_buf, "lmc-weights-equil=%s only possible when lmc-stats = %s or lmc-stats %s",
+ elmceq_names[elmceqWLDELTA], elamstats_names[elamstatsWL], elamstats_names[elamstatsWWL]);
+ CHECK((expand->elmceq == elmceqWLDELTA) && (!EWL(expand->elamstats)));
+
+ sprintf(err_buf, "lmc-repeats (%d) must be greater than 0", expand->lmc_repeats);
+ CHECK((expand->lmc_repeats <= 0));
+ sprintf(err_buf, "minimum-var-min (%d) must be greater than 0", expand->minvarmin);
+ CHECK((expand->minvarmin <= 0));
+ sprintf(err_buf, "weight-c-range (%d) must be greater or equal to 0", expand->c_range);
+ CHECK((expand->c_range < 0));
+ sprintf(err_buf, "init-lambda-state (%d) must be zero if lmc-forced-nstart (%d)> 0 and lmc-move != 'no'",
+ fep->init_fep_state, expand->lmc_forced_nstart);
+ CHECK((fep->init_fep_state != 0) && (expand->lmc_forced_nstart > 0) && (expand->elmcmove != elmcmoveNO));
+ sprintf(err_buf, "lmc-forced-nstart (%d) must not be negative", expand->lmc_forced_nstart);
+ CHECK((expand->lmc_forced_nstart < 0));
+ sprintf(err_buf, "init-lambda-state (%d) must be in the interval [0,number of lambdas)", fep->init_fep_state);
+ CHECK((fep->init_fep_state < 0) || (fep->init_fep_state >= fep->n_lambda));
+
+ sprintf(err_buf, "init-wl-delta (%f) must be greater than or equal to 0", expand->init_wl_delta);
+ CHECK((expand->init_wl_delta < 0));
+ sprintf(err_buf, "wl-ratio (%f) must be between 0 and 1", expand->wl_ratio);
+ CHECK((expand->wl_ratio <= 0) || (expand->wl_ratio >= 1));
+ sprintf(err_buf, "wl-scale (%f) must be between 0 and 1", expand->wl_scale);
+ CHECK((expand->wl_scale <= 0) || (expand->wl_scale >= 1));
+
+ /* if there is no temperature control, we need to specify an MC temperature */
+ sprintf(err_buf, "If there is no temperature control, and lmc-mcmove!= 'no',mc_temperature must be set to a positive number");
+ if (expand->nstTij > 0)
+ {
+ sprintf(err_buf, "nst-transition-matrix (%d) must be an integer multiple of nstlog (%d)",
+ expand->nstTij, ir->nstlog);
+ CHECK((mod(expand->nstTij, ir->nstlog) != 0));
+ }
+ }
+
+ /* PBC/WALLS */
+ sprintf(err_buf, "walls only work with pbc=%s", epbc_names[epbcXY]);
+ CHECK(ir->nwall && ir->ePBC != epbcXY);
+
+ /* VACUUM STUFF */
+ if (ir->ePBC != epbcXYZ && ir->nwall != 2)
+ {
+ if (ir->ePBC == epbcNONE)
+ {
+ if (ir->epc != epcNO)
+ {
+ warning(wi, "Turning off pressure coupling for vacuum system");
+ ir->epc = epcNO;
+ }
+ }
+ else
+ {
+ sprintf(err_buf, "Can not have pressure coupling with pbc=%s",
+ epbc_names[ir->ePBC]);
+ CHECK(ir->epc != epcNO);
+ }
+ sprintf(err_buf, "Can not have Ewald with pbc=%s", epbc_names[ir->ePBC]);
+ CHECK(EEL_FULL(ir->coulombtype));
+
+ sprintf(err_buf, "Can not have dispersion correction with pbc=%s",
+ epbc_names[ir->ePBC]);
+ CHECK(ir->eDispCorr != edispcNO);
+ }
+
+ if (ir->rlist == 0.0)
+ {
+ sprintf(err_buf, "can only have neighborlist cut-off zero (=infinite)\n"
+ "with coulombtype = %s or coulombtype = %s\n"
+ "without periodic boundary conditions (pbc = %s) and\n"
+ "rcoulomb and rvdw set to zero",
+ eel_names[eelCUT], eel_names[eelUSER], epbc_names[epbcNONE]);
+ CHECK(((ir->coulombtype != eelCUT) && (ir->coulombtype != eelUSER)) ||
+ (ir->ePBC != epbcNONE) ||
+ (ir->rcoulomb != 0.0) || (ir->rvdw != 0.0));
+
+ if (ir->nstlist < 0)
+ {
+ warning_error(wi, "Can not have heuristic neighborlist updates without cut-off");
+ }
+ if (ir->nstlist > 0)
+ {
+ warning_note(wi, "Simulating without cut-offs can be (slightly) faster with nstlist=0, nstype=simple and only one MPI rank");
+ }
+ }
+
+ /* COMM STUFF */
+ if (ir->nstcomm == 0)
+ {
+ ir->comm_mode = ecmNO;
+ }
+ if (ir->comm_mode != ecmNO)
+ {
+ if (ir->nstcomm < 0)
+ {
+ warning(wi, "If you want to remove the rotation around the center of mass, you should set comm_mode = Angular instead of setting nstcomm < 0. nstcomm is modified to its absolute value");
+ ir->nstcomm = abs(ir->nstcomm);
+ }
+
+ if (ir->nstcalcenergy > 0 && ir->nstcomm < ir->nstcalcenergy)
+ {
+ warning_note(wi, "nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting nstcomm to nstcalcenergy");
+ ir->nstcomm = ir->nstcalcenergy;
+ }
+
+ if (ir->comm_mode == ecmANGULAR)
+ {
+ sprintf(err_buf, "Can not remove the rotation around the center of mass with periodic molecules");
+ CHECK(ir->bPeriodicMols);
+ if (ir->ePBC != epbcNONE)
+ {
+ warning(wi, "Removing the rotation around the center of mass in a periodic system (this is not a problem when you have only one molecule).");
+ }
+ }
+ }
+
+ if (EI_STATE_VELOCITY(ir->eI) && ir->ePBC == epbcNONE && ir->comm_mode != ecmANGULAR)
+ {
+ warning_note(wi, "Tumbling and or flying ice-cubes: We are not removing rotation around center of mass in a non-periodic system. You should probably set comm_mode = ANGULAR.");
+ }
+
+ sprintf(err_buf, "Twin-range neighbour searching (NS) with simple NS"
+ " algorithm not implemented");
+ CHECK(((ir->rcoulomb > ir->rlist) || (ir->rvdw > ir->rlist))
+ && (ir->ns_type == ensSIMPLE));
+
+ /* TEMPERATURE COUPLING */
+ if (ir->etc == etcYES)
+ {
+ ir->etc = etcBERENDSEN;
+ warning_note(wi, "Old option for temperature coupling given: "
+ "changing \"yes\" to \"Berendsen\"\n");
+ }
+
+ if ((ir->etc == etcNOSEHOOVER) || (ir->epc == epcMTTK))
+ {
+ if (ir->opts.nhchainlength < 1)
+ {
+ sprintf(warn_buf, "number of Nose-Hoover chains (currently %d) cannot be less than 1,reset to 1\n", ir->opts.nhchainlength);
+ ir->opts.nhchainlength = 1;
+ warning(wi, warn_buf);
+ }
+
+ if (ir->etc == etcNOSEHOOVER && !EI_VV(ir->eI) && ir->opts.nhchainlength > 1)
+ {
+ warning_note(wi, "leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1");
+ ir->opts.nhchainlength = 1;
+ }
+ }
+ else
+ {
+ ir->opts.nhchainlength = 0;
+ }
+
+ if (ir->eI == eiVVAK)
+ {
+ sprintf(err_buf, "%s implemented primarily for validation, and requires nsttcouple = 1 and nstpcouple = 1.",
+ ei_names[eiVVAK]);
+ CHECK((ir->nsttcouple != 1) || (ir->nstpcouple != 1));
+ }
+
+ if (ETC_ANDERSEN(ir->etc))
+ {
+ sprintf(err_buf, "%s temperature control not supported for integrator %s.", etcoupl_names[ir->etc], ei_names[ir->eI]);
+ CHECK(!(EI_VV(ir->eI)));
+
+ if (ir->nstcomm > 0 && (ir->etc == etcANDERSEN))
+ {
+ sprintf(warn_buf, "Center of mass removal not necessary for %s. All velocities of coupled groups are rerandomized periodically, so flying ice cube errors will not occur.", etcoupl_names[ir->etc]);
+ warning_note(wi, warn_buf);
+ }
+
+ sprintf(err_buf, "nstcomm must be 1, not %d for %s, as velocities of atoms in coupled groups are randomized every time step", ir->nstcomm, etcoupl_names[ir->etc]);
+ CHECK(ir->nstcomm > 1 && (ir->etc == etcANDERSEN));
+ }
+
+ if (ir->etc == etcBERENDSEN)
+ {
+ sprintf(warn_buf, "The %s thermostat does not generate the correct kinetic energy distribution. You might want to consider using the %s thermostat.",
+ ETCOUPLTYPE(ir->etc), ETCOUPLTYPE(etcVRESCALE));
+ warning_note(wi, warn_buf);
+ }
+
+ if ((ir->etc == etcNOSEHOOVER || ETC_ANDERSEN(ir->etc))
+ && ir->epc == epcBERENDSEN)
+ {
+ sprintf(warn_buf, "Using Berendsen pressure coupling invalidates the "
+ "true ensemble for the thermostat");
+ warning(wi, warn_buf);
+ }
+
+ /* PRESSURE COUPLING */
+ if (ir->epc == epcISOTROPIC)
+ {
+ ir->epc = epcBERENDSEN;
+ warning_note(wi, "Old option for pressure coupling given: "
+ "changing \"Isotropic\" to \"Berendsen\"\n");
+ }
+
+ if (ir->epc != epcNO)
+ {
+ dt_pcoupl = ir->nstpcouple*ir->delta_t;
+
+ sprintf(err_buf, "tau-p must be > 0 instead of %g\n", ir->tau_p);
+ CHECK(ir->tau_p <= 0);
+
+ if (ir->tau_p/dt_pcoupl < pcouple_min_integration_steps(ir->epc))
+ {
+ sprintf(warn_buf, "For proper integration of the %s barostat, tau-p (%g) should be at least %d times larger than nstpcouple*dt (%g)",
+ EPCOUPLTYPE(ir->epc), ir->tau_p, pcouple_min_integration_steps(ir->epc), dt_pcoupl);
+ warning(wi, warn_buf);
+ }
+
+ sprintf(err_buf, "compressibility must be > 0 when using pressure"
+ " coupling %s\n", EPCOUPLTYPE(ir->epc));
+ CHECK(ir->compress[XX][XX] < 0 || ir->compress[YY][YY] < 0 ||
+ ir->compress[ZZ][ZZ] < 0 ||
+ (trace(ir->compress) == 0 && ir->compress[YY][XX] <= 0 &&
+ ir->compress[ZZ][XX] <= 0 && ir->compress[ZZ][YY] <= 0));
+
+ if (epcPARRINELLORAHMAN == ir->epc && opts->bGenVel)
+ {
+ sprintf(warn_buf,
+ "You are generating velocities so I am assuming you "
+ "are equilibrating a system. You are using "
+ "%s pressure coupling, but this can be "
+ "unstable for equilibration. If your system crashes, try "
+ "equilibrating first with Berendsen pressure coupling. If "
+ "you are not equilibrating the system, you can probably "
+ "ignore this warning.",
+ epcoupl_names[ir->epc]);
+ warning(wi, warn_buf);
+ }
+ }
+
+ if (EI_VV(ir->eI))
+ {
+ if (ir->epc > epcNO)
+ {
+ if ((ir->epc != epcBERENDSEN) && (ir->epc != epcMTTK))
+ {
+ warning_error(wi, "for md-vv and md-vv-avek, can only use Berendsen and Martyna-Tuckerman-Tobias-Klein (MTTK) equations for pressure control; MTTK is equivalent to Parrinello-Rahman.");
+ }
+ }
+ }
+ else
+ {
+ if (ir->epc == epcMTTK)
+ {
+ warning_error(wi, "MTTK pressure coupling requires a Velocity-verlet integrator");
+ }
+ }
+
+ /* ELECTROSTATICS */
+ /* More checks are in triple check (grompp.c) */
+
+ if (ir->coulombtype == eelSWITCH)
+ {
+ sprintf(warn_buf, "coulombtype = %s is only for testing purposes and can lead to serious "
+ "artifacts, advice: use coulombtype = %s",
+ eel_names[ir->coulombtype],
+ eel_names[eelRF_ZERO]);
+ warning(wi, warn_buf);
+ }
+
+ if (ir->epsilon_r != 1 && ir->implicit_solvent == eisGBSA)
+ {
+ sprintf(warn_buf, "epsilon-r = %g with GB implicit solvent, will use this value for inner dielectric", ir->epsilon_r);
+ warning_note(wi, warn_buf);
+ }
+
+ if (EEL_RF(ir->coulombtype) && ir->epsilon_rf == 1 && ir->epsilon_r != 1)
+ {
+ sprintf(warn_buf, "epsilon-r = %g and epsilon-rf = 1 with reaction field, proceeding assuming old format and exchanging epsilon-r and epsilon-rf", ir->epsilon_r);
+ warning(wi, warn_buf);
+ ir->epsilon_rf = ir->epsilon_r;
+ ir->epsilon_r = 1.0;
+ }
+
+ if (getenv("GALACTIC_DYNAMICS") == NULL)
+ {
+ sprintf(err_buf, "epsilon-r must be >= 0 instead of %g\n", ir->epsilon_r);
+ CHECK(ir->epsilon_r < 0);
+ }
+
+ if (EEL_RF(ir->coulombtype))
+ {
+ /* reaction field (at the cut-off) */
+
+ if (ir->coulombtype == eelRF_ZERO)
+ {
+ sprintf(warn_buf, "With coulombtype = %s, epsilon-rf must be 0, assuming you meant epsilon_rf=0",
+ eel_names[ir->coulombtype]);
+ CHECK(ir->epsilon_rf != 0);
+ ir->epsilon_rf = 0.0;
+ }
+
+ sprintf(err_buf, "epsilon-rf must be >= epsilon-r");
+ CHECK((ir->epsilon_rf < ir->epsilon_r && ir->epsilon_rf != 0) ||
+ (ir->epsilon_r == 0));
+ if (ir->epsilon_rf == ir->epsilon_r)
+ {
+ sprintf(warn_buf, "Using epsilon-rf = epsilon-r with %s does not make sense",
+ eel_names[ir->coulombtype]);
+ warning(wi, warn_buf);
+ }
+ }
+ /* Allow rlist>rcoulomb for tabulated long range stuff. This just
+ * means the interaction is zero outside rcoulomb, but it helps to
+ * provide accurate energy conservation.
+ */
+ if (ir_coulomb_might_be_zero_at_cutoff(ir))
+ {
+ if (ir_coulomb_switched(ir))
+ {
+ sprintf(err_buf,
+ "With coulombtype = %s rcoulomb_switch must be < rcoulomb. Or, better: Use the potential modifier options!",
+ eel_names[ir->coulombtype]);
+ CHECK(ir->rcoulomb_switch >= ir->rcoulomb);
+ }
+ }
+ else if (ir->coulombtype == eelCUT || EEL_RF(ir->coulombtype))
+ {
+ if (ir->cutoff_scheme == ecutsGROUP && ir->coulomb_modifier == eintmodNONE)
+ {
+ sprintf(err_buf, "With coulombtype = %s, rcoulomb should be >= rlist unless you use a potential modifier",
+ eel_names[ir->coulombtype]);
+ CHECK(ir->rlist > ir->rcoulomb);
+ }
+ }
+
+ if (ir->coulombtype == eelSWITCH || ir->coulombtype == eelSHIFT ||
+ ir->vdwtype == evdwSWITCH || ir->vdwtype == evdwSHIFT)
+ {
+ sprintf(warn_buf,
+ "The switch/shift interaction settings are just for compatibility; you will get better "
+ "performance from applying potential modifiers to your interactions!\n");
+ warning_note(wi, warn_buf);
+ }
+
+ if (ir->coulombtype == eelPMESWITCH || ir->coulomb_modifier == eintmodPOTSWITCH)
+ {
+ if (ir->rcoulomb_switch/ir->rcoulomb < 0.9499)
+ {
+ real percentage = 100*(ir->rcoulomb-ir->rcoulomb_switch)/ir->rcoulomb;
+ sprintf(warn_buf, "The switching range for should be 5%% or less (currently %.2f%% using a switching range of %4f-%4f) for accurate electrostatic energies, energy conservation will be good regardless, since ewald_rtol = %g.",
+ percentage, ir->rcoulomb_switch, ir->rcoulomb, ir->ewald_rtol);
+ warning(wi, warn_buf);
+ }
+ }
+
+ if (ir->vdwtype == evdwSWITCH || ir->vdw_modifier == eintmodPOTSWITCH)
+ {
+ if (ir->rvdw_switch == 0)
+ {
+ sprintf(warn_buf, "rvdw-switch is equal 0 even though you are using a switched Lennard-Jones potential. This suggests it was not set in the mdp, which can lead to large energy errors. In GROMACS, 0.05 to 0.1 nm is often a reasonable vdw switching range.");
+ warning(wi, warn_buf);
+ }
+ }
+
+ if (EEL_FULL(ir->coulombtype))
+ {
+ if (ir->coulombtype == eelPMESWITCH || ir->coulombtype == eelPMEUSER ||
+ ir->coulombtype == eelPMEUSERSWITCH)
+ {
+ sprintf(err_buf, "With coulombtype = %s, rcoulomb must be <= rlist",
+ eel_names[ir->coulombtype]);
+ CHECK(ir->rcoulomb > ir->rlist);
+ }
+ else if (ir->cutoff_scheme == ecutsGROUP && ir->coulomb_modifier == eintmodNONE)
+ {
+ if (ir->coulombtype == eelPME || ir->coulombtype == eelP3M_AD)
+ {
+ sprintf(err_buf,
+ "With coulombtype = %s (without modifier), rcoulomb must be equal to rlist,\n"
+ "or rlistlong if nstcalclr=1. For optimal energy conservation,consider using\n"
+ "a potential modifier.", eel_names[ir->coulombtype]);
+ if (ir->nstcalclr == 1)
+ {
+ CHECK(ir->rcoulomb != ir->rlist && ir->rcoulomb != ir->rlistlong);
+ }
+ else
+ {
+ CHECK(ir->rcoulomb != ir->rlist);
+ }
+ }
+ }
+ }
+
+ if (EEL_PME(ir->coulombtype) || EVDW_PME(ir->vdwtype))
+ {
+ if (ir->pme_order < 3)
+ {
+ warning_error(wi, "pme-order can not be smaller than 3");
+ }
+ }
+
+ if (ir->nwall == 2 && EEL_FULL(ir->coulombtype))
+ {
+ if (ir->ewald_geometry == eewg3D)
+ {
+ sprintf(warn_buf, "With pbc=%s you should use ewald-geometry=%s",
+ epbc_names[ir->ePBC], eewg_names[eewg3DC]);
+ warning(wi, warn_buf);
+ }
+ /* This check avoids extra pbc coding for exclusion corrections */
+ sprintf(err_buf, "wall-ewald-zfac should be >= 2");
+ CHECK(ir->wall_ewald_zfac < 2);
+ }
+
+ if (ir_vdw_switched(ir))
+ {
+ sprintf(err_buf, "With switched vdw forces or potentials, rvdw-switch must be < rvdw");
+ CHECK(ir->rvdw_switch >= ir->rvdw);
+
+ if (ir->rvdw_switch < 0.5*ir->rvdw)
+ {
+ sprintf(warn_buf, "You are applying a switch function to vdw forces or potentials from %g to %g nm, which is more than half the interaction range, whereas switch functions are intended to act only close to the cut-off.",
+ ir->rvdw_switch, ir->rvdw);
+ warning_note(wi, warn_buf);
+ }
+ }
+ else if (ir->vdwtype == evdwCUT || ir->vdwtype == evdwPME)
+ {
+ if (ir->cutoff_scheme == ecutsGROUP && ir->vdw_modifier == eintmodNONE)
+ {
+ sprintf(err_buf, "With vdwtype = %s, rvdw must be >= rlist unless you use a potential modifier", evdw_names[ir->vdwtype]);
+ CHECK(ir->rlist > ir->rvdw);
+ }
+ }
+
+ if (ir->vdwtype == evdwPME)
+ {
+ if (!(ir->vdw_modifier == eintmodNONE || ir->vdw_modifier == eintmodPOTSHIFT))
+ {
+ sprintf(err_buf, "With vdwtype = %s, the only supported modifiers are %s a\
+nd %s",
+ evdw_names[ir->vdwtype],
+ eintmod_names[eintmodPOTSHIFT],
+ eintmod_names[eintmodNONE]);
+ }
+ }
+
+ if (ir->cutoff_scheme == ecutsGROUP)
+ {
+ if (((ir->coulomb_modifier != eintmodNONE && ir->rcoulomb == ir->rlist) ||
+ (ir->vdw_modifier != eintmodNONE && ir->rvdw == ir->rlist)) &&
+ ir->nstlist != 1)
+ {
+ warning_note(wi, "With exact cut-offs, rlist should be "
+ "larger than rcoulomb and rvdw, so that there "
+ "is a buffer region for particle motion "
+ "between neighborsearch steps");
+ }
+
+ if (ir_coulomb_is_zero_at_cutoff(ir) && ir->rlistlong <= ir->rcoulomb)
+ {
+ sprintf(warn_buf, "For energy conservation with switch/shift potentials, %s should be 0.1 to 0.3 nm larger than rcoulomb.",
+ IR_TWINRANGE(*ir) ? "rlistlong" : "rlist");
+ warning_note(wi, warn_buf);
+ }
+ if (ir_vdw_switched(ir) && (ir->rlistlong <= ir->rvdw))
+ {
+ sprintf(warn_buf, "For energy conservation with switch/shift potentials, %s should be 0.1 to 0.3 nm larger than rvdw.",
+ IR_TWINRANGE(*ir) ? "rlistlong" : "rlist");
+ warning_note(wi, warn_buf);
+ }
+ }
+
+ if (ir->vdwtype == evdwUSER && ir->eDispCorr != edispcNO)
+ {
+ warning_note(wi, "You have selected user tables with dispersion correction, the dispersion will be corrected to -C6/r^6 beyond rvdw_switch (the tabulated interaction between rvdw_switch and rvdw will not be double counted). Make sure that you really want dispersion correction to -C6/r^6.");
+ }
+
+ if (ir->nstlist == -1)
+ {
+ sprintf(err_buf, "With nstlist=-1 rvdw and rcoulomb should be smaller than rlist to account for diffusion and possibly charge-group radii");
+ CHECK(ir->rvdw >= ir->rlist || ir->rcoulomb >= ir->rlist);
+ }
+ sprintf(err_buf, "nstlist can not be smaller than -1");
+ CHECK(ir->nstlist < -1);
+
+ if (ir->eI == eiLBFGS && (ir->coulombtype == eelCUT || ir->vdwtype == evdwCUT)
+ && ir->rvdw != 0)
+ {
+ warning(wi, "For efficient BFGS minimization, use switch/shift/pme instead of cut-off.");
+ }
+
+ if (ir->eI == eiLBFGS && ir->nbfgscorr <= 0)
+ {
+ warning(wi, "Using L-BFGS with nbfgscorr<=0 just gets you steepest descent.");
+ }
+
+ /* ENERGY CONSERVATION */
+ if (ir_NVE(ir) && ir->cutoff_scheme == ecutsGROUP)
+ {
+ if (!ir_vdw_might_be_zero_at_cutoff(ir) && ir->rvdw > 0 && ir->vdw_modifier == eintmodNONE)
+ {
+ sprintf(warn_buf, "You are using a cut-off for VdW interactions with NVE, for good energy conservation use vdwtype = %s (possibly with DispCorr)",
+ evdw_names[evdwSHIFT]);
+ warning_note(wi, warn_buf);
+ }
+ if (!ir_coulomb_might_be_zero_at_cutoff(ir) && ir->rcoulomb > 0)
+ {
+ sprintf(warn_buf, "You are using a cut-off for electrostatics with NVE, for good energy conservation use coulombtype = %s or %s",
+ eel_names[eelPMESWITCH], eel_names[eelRF_ZERO]);
+ warning_note(wi, warn_buf);
+ }
+ }
+
++ if (EI_VV(ir->eI) && IR_TWINRANGE(*ir) && ir->nstlist > 1)
++ {
++ sprintf(warn_buf, "Twin-range multiple time stepping does not work with integrator %s.", ei_names[ir->eI]);
++ warning_error(wi, warn_buf);
++ }
++
+ /* IMPLICIT SOLVENT */
+ if (ir->coulombtype == eelGB_NOTUSED)
+ {
+ ir->coulombtype = eelCUT;
+ ir->implicit_solvent = eisGBSA;
+ fprintf(stderr, "Note: Old option for generalized born electrostatics given:\n"
+ "Changing coulombtype from \"generalized-born\" to \"cut-off\" and instead\n"
+ "setting implicit-solvent value to \"GBSA\" in input section.\n");
+ }
+
+ if (ir->sa_algorithm == esaSTILL)
+ {
+ sprintf(err_buf, "Still SA algorithm not available yet, use %s or %s instead\n", esa_names[esaAPPROX], esa_names[esaNO]);
+ CHECK(ir->sa_algorithm == esaSTILL);
+ }
+
+ if (ir->implicit_solvent == eisGBSA)
+ {
+ sprintf(err_buf, "With GBSA implicit solvent, rgbradii must be equal to rlist.");
+ CHECK(ir->rgbradii != ir->rlist);
+
+ if (ir->coulombtype != eelCUT)
+ {
+ sprintf(err_buf, "With GBSA, coulombtype must be equal to %s\n", eel_names[eelCUT]);
+ CHECK(ir->coulombtype != eelCUT);
+ }
+ if (ir->vdwtype != evdwCUT)
+ {
+ sprintf(err_buf, "With GBSA, vdw-type must be equal to %s\n", evdw_names[evdwCUT]);
+ CHECK(ir->vdwtype != evdwCUT);
+ }
+ if (ir->nstgbradii < 1)
+ {
+ sprintf(warn_buf, "Using GBSA with nstgbradii<1, setting nstgbradii=1");
+ warning_note(wi, warn_buf);
+ ir->nstgbradii = 1;
+ }
+ if (ir->sa_algorithm == esaNO)
+ {
+ sprintf(warn_buf, "No SA (non-polar) calculation requested together with GB. Are you sure this is what you want?\n");
+ warning_note(wi, warn_buf);
+ }
+ if (ir->sa_surface_tension < 0 && ir->sa_algorithm != esaNO)
+ {
+ sprintf(warn_buf, "Value of sa_surface_tension is < 0. Changing it to 2.05016 or 2.25936 kJ/nm^2/mol for Still and HCT/OBC respectively\n");
+ warning_note(wi, warn_buf);
+
+ if (ir->gb_algorithm == egbSTILL)
+ {
+ ir->sa_surface_tension = 0.0049 * CAL2JOULE * 100;
+ }
+ else
+ {
+ ir->sa_surface_tension = 0.0054 * CAL2JOULE * 100;
+ }
+ }
+ if (ir->sa_surface_tension == 0 && ir->sa_algorithm != esaNO)
+ {
+ sprintf(err_buf, "Surface tension set to 0 while SA-calculation requested\n");
+ CHECK(ir->sa_surface_tension == 0 && ir->sa_algorithm != esaNO);
+ }
+
+ }
+
+ if (ir->bAdress)
+ {
+ if (ir->cutoff_scheme != ecutsGROUP)
+ {
+ warning_error(wi, "AdresS simulation supports only cutoff-scheme=group");
+ }
+ if (!EI_SD(ir->eI))
+ {
+ warning_error(wi, "AdresS simulation supports only stochastic dynamics");
+ }
+ if (ir->epc != epcNO)
+ {
+ warning_error(wi, "AdresS simulation does not support pressure coupling");
+ }
+ if (EEL_FULL(ir->coulombtype))
+ {
+ warning_error(wi, "AdresS simulation does not support long-range electrostatics");
+ }
+ }
+}
+
+/* count the number of text elemets separated by whitespace in a string.
+ str = the input string
+ maxptr = the maximum number of allowed elements
+ ptr = the output array of pointers to the first character of each element
+ returns: the number of elements. */
+int str_nelem(const char *str, int maxptr, char *ptr[])
+{
+ int np = 0;
+ char *copy0, *copy;
+
+ copy0 = strdup(str);
+ copy = copy0;
+ ltrim(copy);
+ while (*copy != '\0')
+ {
+ if (np >= maxptr)
+ {
+ gmx_fatal(FARGS, "Too many groups on line: '%s' (max is %d)",
+ str, maxptr);
+ }
+ if (ptr)
+ {
+ ptr[np] = copy;
+ }
+ np++;
+ while ((*copy != '\0') && !isspace(*copy))
+ {
+ copy++;
+ }
+ if (*copy != '\0')
+ {
+ *copy = '\0';
+ copy++;
+ }
+ ltrim(copy);
+ }
+ if (ptr == NULL)
+ {
+ sfree(copy0);
+ }
+
+ return np;
+}
+
+/* interpret a number of doubles from a string and put them in an array,
+ after allocating space for them.
+ str = the input string
+ n = the (pre-allocated) number of doubles read
+ r = the output array of doubles. */
+static void parse_n_real(char *str, int *n, real **r)
+{
+ char *ptr[MAXPTR];
+ int i;
+
+ *n = str_nelem(str, MAXPTR, ptr);
+
+ snew(*r, *n);
+ for (i = 0; i < *n; i++)
+ {
+ (*r)[i] = strtod(ptr[i], NULL);
+ }
+}
+
+static void do_fep_params(t_inputrec *ir, char fep_lambda[][STRLEN], char weights[STRLEN])
+{
+
+ int i, j, max_n_lambda, nweights, nfep[efptNR];
+ t_lambda *fep = ir->fepvals;
+ t_expanded *expand = ir->expandedvals;
+ real **count_fep_lambdas;
+ gmx_bool bOneLambda = TRUE;
+
+ snew(count_fep_lambdas, efptNR);
+
+ /* FEP input processing */
+ /* first, identify the number of lambda values for each type.
+ All that are nonzero must have the same number */
+
+ for (i = 0; i < efptNR; i++)
+ {
+ parse_n_real(fep_lambda[i], &(nfep[i]), &(count_fep_lambdas[i]));
+ }
+
+ /* now, determine the number of components. All must be either zero, or equal. */
+
+ max_n_lambda = 0;
+ for (i = 0; i < efptNR; i++)
+ {
+ if (nfep[i] > max_n_lambda)
+ {
+ max_n_lambda = nfep[i]; /* here's a nonzero one. All of them
+ must have the same number if its not zero.*/
+ break;
+ }
+ }
+
+ for (i = 0; i < efptNR; i++)
+ {
+ if (nfep[i] == 0)
+ {
+ ir->fepvals->separate_dvdl[i] = FALSE;
+ }
+ else if (nfep[i] == max_n_lambda)
+ {
+ if (i != efptTEMPERATURE) /* we treat this differently -- not really a reason to compute the derivative with
+ respect to the temperature currently */
+ {
+ ir->fepvals->separate_dvdl[i] = TRUE;
+ }
+ }
+ else
+ {
+ gmx_fatal(FARGS, "Number of lambdas (%d) for FEP type %s not equal to number of other types (%d)",
+ nfep[i], efpt_names[i], max_n_lambda);
+ }
+ }
+ /* we don't print out dhdl if the temperature is changing, since we can't correctly define dhdl in this case */
+ ir->fepvals->separate_dvdl[efptTEMPERATURE] = FALSE;
+
+ /* the number of lambdas is the number we've read in, which is either zero
+ or the same for all */
+ fep->n_lambda = max_n_lambda;
+
+ /* allocate space for the array of lambda values */
+ snew(fep->all_lambda, efptNR);
+ /* if init_lambda is defined, we need to set lambda */
+ if ((fep->init_lambda > 0) && (fep->n_lambda == 0))
+ {
+ ir->fepvals->separate_dvdl[efptFEP] = TRUE;
+ }
+ /* otherwise allocate the space for all of the lambdas, and transfer the data */
+ for (i = 0; i < efptNR; i++)
+ {
+ snew(fep->all_lambda[i], fep->n_lambda);
+ if (nfep[i] > 0) /* if it's zero, then the count_fep_lambda arrays
+ are zero */
+ {
+ for (j = 0; j < fep->n_lambda; j++)
+ {
+ fep->all_lambda[i][j] = (double)count_fep_lambdas[i][j];
+ }
+ sfree(count_fep_lambdas[i]);
+ }
+ }
+ sfree(count_fep_lambdas);
+
+ /* "fep-vals" is either zero or the full number. If zero, we'll need to define fep-lambdas for internal
+ bookkeeping -- for now, init_lambda */
+
+ if ((nfep[efptFEP] == 0) && (fep->init_lambda >= 0))
+ {
+ for (i = 0; i < fep->n_lambda; i++)
+ {
+ fep->all_lambda[efptFEP][i] = fep->init_lambda;
+ }
+ }
+
+ /* check to see if only a single component lambda is defined, and soft core is defined.
+ In this case, turn on coulomb soft core */
+
+ if (max_n_lambda == 0)
+ {
+ bOneLambda = TRUE;
+ }
+ else
+ {
+ for (i = 0; i < efptNR; i++)
+ {
+ if ((nfep[i] != 0) && (i != efptFEP))
+ {
+ bOneLambda = FALSE;
+ }
+ }
+ }
+ if ((bOneLambda) && (fep->sc_alpha > 0))
+ {
+ fep->bScCoul = TRUE;
+ }
+
+ /* Fill in the others with the efptFEP if they are not explicitly
+ specified (i.e. nfep[i] == 0). This means if fep is not defined,
+ they are all zero. */
+
+ for (i = 0; i < efptNR; i++)
+ {
+ if ((nfep[i] == 0) && (i != efptFEP))
+ {
+ for (j = 0; j < fep->n_lambda; j++)
+ {
+ fep->all_lambda[i][j] = fep->all_lambda[efptFEP][j];
+ }
+ }
+ }
+
+
+ /* make it easier if sc_r_power = 48 by increasing it to the 4th power, to be in the right scale. */
+ if (fep->sc_r_power == 48)
+ {
+ if (fep->sc_alpha > 0.1)
+ {
+ gmx_fatal(FARGS, "sc_alpha (%f) for sc_r_power = 48 should usually be between 0.001 and 0.004", fep->sc_alpha);
+ }
+ }
+
+ expand = ir->expandedvals;
+ /* now read in the weights */
+ parse_n_real(weights, &nweights, &(expand->init_lambda_weights));
+ if (nweights == 0)
+ {
+ snew(expand->init_lambda_weights, fep->n_lambda); /* initialize to zero */
+ }
+ else if (nweights != fep->n_lambda)
+ {
+ gmx_fatal(FARGS, "Number of weights (%d) is not equal to number of lambda values (%d)",
+ nweights, fep->n_lambda);
+ }
+ if ((expand->nstexpanded < 0) && (ir->efep != efepNO))
+ {
+ expand->nstexpanded = fep->nstdhdl;
+ /* if you don't specify nstexpanded when doing expanded ensemble free energy calcs, it is set to nstdhdl */
+ }
+ if ((expand->nstexpanded < 0) && ir->bSimTemp)
+ {
+ expand->nstexpanded = 2*(int)(ir->opts.tau_t[0]/ir->delta_t);
+ /* if you don't specify nstexpanded when doing expanded ensemble simulated tempering, it is set to
+ 2*tau_t just to be careful so it's not to frequent */
+ }
+}
+
+
+static void do_simtemp_params(t_inputrec *ir)
+{
+
+ snew(ir->simtempvals->temperatures, ir->fepvals->n_lambda);
+ GetSimTemps(ir->fepvals->n_lambda, ir->simtempvals, ir->fepvals->all_lambda[efptTEMPERATURE]);
+
+ return;
+}
+
+static void do_wall_params(t_inputrec *ir,
+ char *wall_atomtype, char *wall_density,
+ t_gromppopts *opts)
+{
+ int nstr, i;
+ char *names[MAXPTR];
+ double dbl;
+
+ opts->wall_atomtype[0] = NULL;
+ opts->wall_atomtype[1] = NULL;
+
+ ir->wall_atomtype[0] = -1;
+ ir->wall_atomtype[1] = -1;
+ ir->wall_density[0] = 0;
+ ir->wall_density[1] = 0;
+
+ if (ir->nwall > 0)
+ {
+ nstr = str_nelem(wall_atomtype, MAXPTR, names);
+ if (nstr != ir->nwall)
+ {
+ gmx_fatal(FARGS, "Expected %d elements for wall_atomtype, found %d",
+ ir->nwall, nstr);
+ }
+ for (i = 0; i < ir->nwall; i++)
+ {
+ opts->wall_atomtype[i] = strdup(names[i]);
+ }
+
+ if (ir->wall_type == ewt93 || ir->wall_type == ewt104)
+ {
+ nstr = str_nelem(wall_density, MAXPTR, names);
+ if (nstr != ir->nwall)
+ {
+ gmx_fatal(FARGS, "Expected %d elements for wall-density, found %d", ir->nwall, nstr);
+ }
+ for (i = 0; i < ir->nwall; i++)
+ {
+ sscanf(names[i], "%lf", &dbl);
+ if (dbl <= 0)
+ {
+ gmx_fatal(FARGS, "wall-density[%d] = %f\n", i, dbl);
+ }
+ ir->wall_density[i] = dbl;
+ }
+ }
+ }
+}
+
+static void add_wall_energrps(gmx_groups_t *groups, int nwall, t_symtab *symtab)
+{
+ int i;
+ t_grps *grps;
+ char str[STRLEN];
+
+ if (nwall > 0)
+ {
+ srenew(groups->grpname, groups->ngrpname+nwall);
+ grps = &(groups->grps[egcENER]);
+ srenew(grps->nm_ind, grps->nr+nwall);
+ for (i = 0; i < nwall; i++)
+ {
+ sprintf(str, "wall%d", i);
+ groups->grpname[groups->ngrpname] = put_symtab(symtab, str);
+ grps->nm_ind[grps->nr++] = groups->ngrpname++;
+ }
+ }
+}
+
+void read_expandedparams(int *ninp_p, t_inpfile **inp_p,
+ t_expanded *expand, warninp_t wi)
+{
+ int ninp, nerror = 0;
+ t_inpfile *inp;
+
+ ninp = *ninp_p;
+ inp = *inp_p;
+
+ /* read expanded ensemble parameters */
+ CCTYPE ("expanded ensemble variables");
+ ITYPE ("nstexpanded", expand->nstexpanded, -1);
+ EETYPE("lmc-stats", expand->elamstats, elamstats_names);
+ EETYPE("lmc-move", expand->elmcmove, elmcmove_names);
+ EETYPE("lmc-weights-equil", expand->elmceq, elmceq_names);
+ ITYPE ("weight-equil-number-all-lambda", expand->equil_n_at_lam, -1);
+ ITYPE ("weight-equil-number-samples", expand->equil_samples, -1);
+ ITYPE ("weight-equil-number-steps", expand->equil_steps, -1);
+ RTYPE ("weight-equil-wl-delta", expand->equil_wl_delta, -1);
+ RTYPE ("weight-equil-count-ratio", expand->equil_ratio, -1);
+ CCTYPE("Seed for Monte Carlo in lambda space");
+ ITYPE ("lmc-seed", expand->lmc_seed, -1);
+ RTYPE ("mc-temperature", expand->mc_temp, -1);
+ ITYPE ("lmc-repeats", expand->lmc_repeats, 1);
+ ITYPE ("lmc-gibbsdelta", expand->gibbsdeltalam, -1);
+ ITYPE ("lmc-forced-nstart", expand->lmc_forced_nstart, 0);
+ EETYPE("symmetrized-transition-matrix", expand->bSymmetrizedTMatrix, yesno_names);
+ ITYPE("nst-transition-matrix", expand->nstTij, -1);
+ ITYPE ("mininum-var-min", expand->minvarmin, 100); /*default is reasonable */
+ ITYPE ("weight-c-range", expand->c_range, 0); /* default is just C=0 */
+ RTYPE ("wl-scale", expand->wl_scale, 0.8);
+ RTYPE ("wl-ratio", expand->wl_ratio, 0.8);
+ RTYPE ("init-wl-delta", expand->init_wl_delta, 1.0);
+ EETYPE("wl-oneovert", expand->bWLoneovert, yesno_names);
+
+ *ninp_p = ninp;
+ *inp_p = inp;
+
+ return;
+}
+
+void get_ir(const char *mdparin, const char *mdparout,
+ t_inputrec *ir, t_gromppopts *opts,
+ warninp_t wi)
+{
+ char *dumstr[2];
+ double dumdub[2][6];
+ t_inpfile *inp;
+ const char *tmp;
+ int i, j, m, ninp;
+ char warn_buf[STRLEN];
+ t_lambda *fep = ir->fepvals;
+ t_expanded *expand = ir->expandedvals;
+
+ init_inputrec_strings();
+ inp = read_inpfile(mdparin, &ninp, wi);
+
+ snew(dumstr[0], STRLEN);
+ snew(dumstr[1], STRLEN);
+
+ if (-1 == search_einp(ninp, inp, "cutoff-scheme"))
+ {
+ sprintf(warn_buf,
+ "%s did not specify a value for the .mdp option "
+ "\"cutoff-scheme\". Probably it was first intended for use "
+ "with GROMACS before 4.6. In 4.6, the Verlet scheme was "
+ "introduced, but the group scheme was still the default. "
+ "The default is now the Verlet scheme, so you will observe "
+ "different behaviour.", mdparin);
+ warning_note(wi, warn_buf);
+ }
+
+ /* remove the following deprecated commands */
+ REM_TYPE("title");
+ REM_TYPE("cpp");
+ REM_TYPE("domain-decomposition");
+ REM_TYPE("andersen-seed");
+ REM_TYPE("dihre");
+ REM_TYPE("dihre-fc");
+ REM_TYPE("dihre-tau");
+ REM_TYPE("nstdihreout");
+ REM_TYPE("nstcheckpoint");
+
+ /* replace the following commands with the clearer new versions*/
+ REPL_TYPE("unconstrained-start", "continuation");
+ REPL_TYPE("foreign-lambda", "fep-lambdas");
+ REPL_TYPE("verlet-buffer-drift", "verlet-buffer-tolerance");
+ REPL_TYPE("nstxtcout", "nstxout-compressed");
+ REPL_TYPE("xtc-grps", "compressed-x-grps");
+ REPL_TYPE("xtc-precision", "compressed-x-precision");
+
+ CCTYPE ("VARIOUS PREPROCESSING OPTIONS");
+ CTYPE ("Preprocessor information: use cpp syntax.");
+ CTYPE ("e.g.: -I/home/joe/doe -I/home/mary/roe");
+ STYPE ("include", opts->include, NULL);
+ CTYPE ("e.g.: -DPOSRES -DFLEXIBLE (note these variable names are case sensitive)");
+ STYPE ("define", opts->define, NULL);
+
+ CCTYPE ("RUN CONTROL PARAMETERS");
+ EETYPE("integrator", ir->eI, ei_names);
+ CTYPE ("Start time and timestep in ps");
+ RTYPE ("tinit", ir->init_t, 0.0);
+ RTYPE ("dt", ir->delta_t, 0.001);
+ STEPTYPE ("nsteps", ir->nsteps, 0);
+ CTYPE ("For exact run continuation or redoing part of a run");
+ STEPTYPE ("init-step", ir->init_step, 0);
+ CTYPE ("Part index is updated automatically on checkpointing (keeps files separate)");
+ ITYPE ("simulation-part", ir->simulation_part, 1);
+ CTYPE ("mode for center of mass motion removal");
+ EETYPE("comm-mode", ir->comm_mode, ecm_names);
+ CTYPE ("number of steps for center of mass motion removal");
+ ITYPE ("nstcomm", ir->nstcomm, 100);
+ CTYPE ("group(s) for center of mass motion removal");
+ STYPE ("comm-grps", is->vcm, NULL);
+
+ CCTYPE ("LANGEVIN DYNAMICS OPTIONS");
+ CTYPE ("Friction coefficient (amu/ps) and random seed");
+ RTYPE ("bd-fric", ir->bd_fric, 0.0);
+ STEPTYPE ("ld-seed", ir->ld_seed, -1);
+
+ /* Em stuff */
+ CCTYPE ("ENERGY MINIMIZATION OPTIONS");
+ CTYPE ("Force tolerance and initial step-size");
+ RTYPE ("emtol", ir->em_tol, 10.0);
+ RTYPE ("emstep", ir->em_stepsize, 0.01);
+ CTYPE ("Max number of iterations in relax-shells");
+ ITYPE ("niter", ir->niter, 20);
+ CTYPE ("Step size (ps^2) for minimization of flexible constraints");
+ RTYPE ("fcstep", ir->fc_stepsize, 0);
+ CTYPE ("Frequency of steepest descents steps when doing CG");
+ ITYPE ("nstcgsteep", ir->nstcgsteep, 1000);
+ ITYPE ("nbfgscorr", ir->nbfgscorr, 10);
+
+ CCTYPE ("TEST PARTICLE INSERTION OPTIONS");
+ RTYPE ("rtpi", ir->rtpi, 0.05);
+
+ /* Output options */
+ CCTYPE ("OUTPUT CONTROL OPTIONS");
+ CTYPE ("Output frequency for coords (x), velocities (v) and forces (f)");
+ ITYPE ("nstxout", ir->nstxout, 0);
+ ITYPE ("nstvout", ir->nstvout, 0);
+ ITYPE ("nstfout", ir->nstfout, 0);
+ ir->nstcheckpoint = 1000;
+ CTYPE ("Output frequency for energies to log file and energy file");
+ ITYPE ("nstlog", ir->nstlog, 1000);
+ ITYPE ("nstcalcenergy", ir->nstcalcenergy, 100);
+ ITYPE ("nstenergy", ir->nstenergy, 1000);
+ CTYPE ("Output frequency and precision for .xtc file");
+ ITYPE ("nstxout-compressed", ir->nstxout_compressed, 0);
+ RTYPE ("compressed-x-precision", ir->x_compression_precision, 1000.0);
+ CTYPE ("This selects the subset of atoms for the compressed");
+ CTYPE ("trajectory file. You can select multiple groups. By");
+ CTYPE ("default, all atoms will be written.");
+ STYPE ("compressed-x-grps", is->x_compressed_groups, NULL);
+ CTYPE ("Selection of energy groups");
+ STYPE ("energygrps", is->energy, NULL);
+
+ /* Neighbor searching */
+ CCTYPE ("NEIGHBORSEARCHING PARAMETERS");
+ CTYPE ("cut-off scheme (Verlet: particle based cut-offs, group: using charge groups)");
+ EETYPE("cutoff-scheme", ir->cutoff_scheme, ecutscheme_names);
+ CTYPE ("nblist update frequency");
+ ITYPE ("nstlist", ir->nstlist, 10);
+ CTYPE ("ns algorithm (simple or grid)");
+ EETYPE("ns-type", ir->ns_type, ens_names);
+ /* set ndelta to the optimal value of 2 */
+ ir->ndelta = 2;
+ CTYPE ("Periodic boundary conditions: xyz, no, xy");
+ EETYPE("pbc", ir->ePBC, epbc_names);
+ EETYPE("periodic-molecules", ir->bPeriodicMols, yesno_names);
+ CTYPE ("Allowed energy error due to the Verlet buffer in kJ/mol/ps per atom,");
+ CTYPE ("a value of -1 means: use rlist");
+ RTYPE("verlet-buffer-tolerance", ir->verletbuf_tol, 0.005);
+ CTYPE ("nblist cut-off");
+ RTYPE ("rlist", ir->rlist, 1.0);
+ CTYPE ("long-range cut-off for switched potentials");
+ RTYPE ("rlistlong", ir->rlistlong, -1);
+ ITYPE ("nstcalclr", ir->nstcalclr, -1);
+
+ /* Electrostatics */
+ CCTYPE ("OPTIONS FOR ELECTROSTATICS AND VDW");
+ CTYPE ("Method for doing electrostatics");
+ EETYPE("coulombtype", ir->coulombtype, eel_names);
+ EETYPE("coulomb-modifier", ir->coulomb_modifier, eintmod_names);
+ CTYPE ("cut-off lengths");
+ RTYPE ("rcoulomb-switch", ir->rcoulomb_switch, 0.0);
+ RTYPE ("rcoulomb", ir->rcoulomb, 1.0);
+ CTYPE ("Relative dielectric constant for the medium and the reaction field");
+ RTYPE ("epsilon-r", ir->epsilon_r, 1.0);
+ RTYPE ("epsilon-rf", ir->epsilon_rf, 0.0);
+ CTYPE ("Method for doing Van der Waals");
+ EETYPE("vdw-type", ir->vdwtype, evdw_names);
+ EETYPE("vdw-modifier", ir->vdw_modifier, eintmod_names);
+ CTYPE ("cut-off lengths");
+ RTYPE ("rvdw-switch", ir->rvdw_switch, 0.0);
+ RTYPE ("rvdw", ir->rvdw, 1.0);
+ CTYPE ("Apply long range dispersion corrections for Energy and Pressure");
+ EETYPE("DispCorr", ir->eDispCorr, edispc_names);
+ CTYPE ("Extension of the potential lookup tables beyond the cut-off");
+ RTYPE ("table-extension", ir->tabext, 1.0);
+ CTYPE ("Separate tables between energy group pairs");
+ STYPE ("energygrp-table", is->egptable, NULL);
+ CTYPE ("Spacing for the PME/PPPM FFT grid");
+ RTYPE ("fourierspacing", ir->fourier_spacing, 0.12);
+ CTYPE ("FFT grid size, when a value is 0 fourierspacing will be used");
+ ITYPE ("fourier-nx", ir->nkx, 0);
+ ITYPE ("fourier-ny", ir->nky, 0);
+ ITYPE ("fourier-nz", ir->nkz, 0);
+ CTYPE ("EWALD/PME/PPPM parameters");
+ ITYPE ("pme-order", ir->pme_order, 4);
+ RTYPE ("ewald-rtol", ir->ewald_rtol, 0.00001);
+ RTYPE ("ewald-rtol-lj", ir->ewald_rtol_lj, 0.001);
+ EETYPE("lj-pme-comb-rule", ir->ljpme_combination_rule, eljpme_names);
+ EETYPE("ewald-geometry", ir->ewald_geometry, eewg_names);
+ RTYPE ("epsilon-surface", ir->epsilon_surface, 0.0);
+ EETYPE("optimize-fft", ir->bOptFFT, yesno_names);
+
+ CCTYPE("IMPLICIT SOLVENT ALGORITHM");
+ EETYPE("implicit-solvent", ir->implicit_solvent, eis_names);
+
+ CCTYPE ("GENERALIZED BORN ELECTROSTATICS");
+ CTYPE ("Algorithm for calculating Born radii");
+ EETYPE("gb-algorithm", ir->gb_algorithm, egb_names);
+ CTYPE ("Frequency of calculating the Born radii inside rlist");
+ ITYPE ("nstgbradii", ir->nstgbradii, 1);
+ CTYPE ("Cutoff for Born radii calculation; the contribution from atoms");
+ CTYPE ("between rlist and rgbradii is updated every nstlist steps");
+ RTYPE ("rgbradii", ir->rgbradii, 1.0);
+ CTYPE ("Dielectric coefficient of the implicit solvent");
+ RTYPE ("gb-epsilon-solvent", ir->gb_epsilon_solvent, 80.0);
+ CTYPE ("Salt concentration in M for Generalized Born models");
+ RTYPE ("gb-saltconc", ir->gb_saltconc, 0.0);
+ CTYPE ("Scaling factors used in the OBC GB model. Default values are OBC(II)");
+ RTYPE ("gb-obc-alpha", ir->gb_obc_alpha, 1.0);
+ RTYPE ("gb-obc-beta", ir->gb_obc_beta, 0.8);
+ RTYPE ("gb-obc-gamma", ir->gb_obc_gamma, 4.85);
+ RTYPE ("gb-dielectric-offset", ir->gb_dielectric_offset, 0.009);
+ EETYPE("sa-algorithm", ir->sa_algorithm, esa_names);
+ CTYPE ("Surface tension (kJ/mol/nm^2) for the SA (nonpolar surface) part of GBSA");
+ CTYPE ("The value -1 will set default value for Still/HCT/OBC GB-models.");
+ RTYPE ("sa-surface-tension", ir->sa_surface_tension, -1);
+
+ /* Coupling stuff */
+ CCTYPE ("OPTIONS FOR WEAK COUPLING ALGORITHMS");
+ CTYPE ("Temperature coupling");
+ EETYPE("tcoupl", ir->etc, etcoupl_names);
+ ITYPE ("nsttcouple", ir->nsttcouple, -1);
+ ITYPE("nh-chain-length", ir->opts.nhchainlength, 10);
+ EETYPE("print-nose-hoover-chain-variables", ir->bPrintNHChains, yesno_names);
+ CTYPE ("Groups to couple separately");
+ STYPE ("tc-grps", is->tcgrps, NULL);
+ CTYPE ("Time constant (ps) and reference temperature (K)");
+ STYPE ("tau-t", is->tau_t, NULL);
+ STYPE ("ref-t", is->ref_t, NULL);
+ CTYPE ("pressure coupling");
+ EETYPE("pcoupl", ir->epc, epcoupl_names);
+ EETYPE("pcoupltype", ir->epct, epcoupltype_names);
+ ITYPE ("nstpcouple", ir->nstpcouple, -1);
+ CTYPE ("Time constant (ps), compressibility (1/bar) and reference P (bar)");
+ RTYPE ("tau-p", ir->tau_p, 1.0);
+ STYPE ("compressibility", dumstr[0], NULL);
+ STYPE ("ref-p", dumstr[1], NULL);
+ CTYPE ("Scaling of reference coordinates, No, All or COM");
+ EETYPE ("refcoord-scaling", ir->refcoord_scaling, erefscaling_names);
+
+ /* QMMM */
+ CCTYPE ("OPTIONS FOR QMMM calculations");
+ EETYPE("QMMM", ir->bQMMM, yesno_names);
+ CTYPE ("Groups treated Quantum Mechanically");
+ STYPE ("QMMM-grps", is->QMMM, NULL);
+ CTYPE ("QM method");
+ STYPE("QMmethod", is->QMmethod, NULL);
+ CTYPE ("QMMM scheme");
+ EETYPE("QMMMscheme", ir->QMMMscheme, eQMMMscheme_names);
+ CTYPE ("QM basisset");
+ STYPE("QMbasis", is->QMbasis, NULL);
+ CTYPE ("QM charge");
+ STYPE ("QMcharge", is->QMcharge, NULL);
+ CTYPE ("QM multiplicity");
+ STYPE ("QMmult", is->QMmult, NULL);
+ CTYPE ("Surface Hopping");
+ STYPE ("SH", is->bSH, NULL);
+ CTYPE ("CAS space options");
+ STYPE ("CASorbitals", is->CASorbitals, NULL);
+ STYPE ("CASelectrons", is->CASelectrons, NULL);
+ STYPE ("SAon", is->SAon, NULL);
+ STYPE ("SAoff", is->SAoff, NULL);
+ STYPE ("SAsteps", is->SAsteps, NULL);
+ CTYPE ("Scale factor for MM charges");
+ RTYPE ("MMChargeScaleFactor", ir->scalefactor, 1.0);
+ CTYPE ("Optimization of QM subsystem");
+ STYPE ("bOPT", is->bOPT, NULL);
+ STYPE ("bTS", is->bTS, NULL);
+
+ /* Simulated annealing */
+ CCTYPE("SIMULATED ANNEALING");
+ CTYPE ("Type of annealing for each temperature group (no/single/periodic)");
+ STYPE ("annealing", is->anneal, NULL);
+ CTYPE ("Number of time points to use for specifying annealing in each group");
+ STYPE ("annealing-npoints", is->anneal_npoints, NULL);
+ CTYPE ("List of times at the annealing points for each group");
+ STYPE ("annealing-time", is->anneal_time, NULL);
+ CTYPE ("Temp. at each annealing point, for each group.");
+ STYPE ("annealing-temp", is->anneal_temp, NULL);
+
+ /* Startup run */
+ CCTYPE ("GENERATE VELOCITIES FOR STARTUP RUN");
+ EETYPE("gen-vel", opts->bGenVel, yesno_names);
+ RTYPE ("gen-temp", opts->tempi, 300.0);
+ ITYPE ("gen-seed", opts->seed, -1);
+
+ /* Shake stuff */
+ CCTYPE ("OPTIONS FOR BONDS");
+ EETYPE("constraints", opts->nshake, constraints);
+ CTYPE ("Type of constraint algorithm");
+ EETYPE("constraint-algorithm", ir->eConstrAlg, econstr_names);
+ CTYPE ("Do not constrain the start configuration");
+ EETYPE("continuation", ir->bContinuation, yesno_names);
+ CTYPE ("Use successive overrelaxation to reduce the number of shake iterations");
+ EETYPE("Shake-SOR", ir->bShakeSOR, yesno_names);
+ CTYPE ("Relative tolerance of shake");
+ RTYPE ("shake-tol", ir->shake_tol, 0.0001);
+ CTYPE ("Highest order in the expansion of the constraint coupling matrix");
+ ITYPE ("lincs-order", ir->nProjOrder, 4);
+ CTYPE ("Number of iterations in the final step of LINCS. 1 is fine for");
+ CTYPE ("normal simulations, but use 2 to conserve energy in NVE runs.");
+ CTYPE ("For energy minimization with constraints it should be 4 to 8.");
+ ITYPE ("lincs-iter", ir->nLincsIter, 1);
+ CTYPE ("Lincs will write a warning to the stderr if in one step a bond");
+ CTYPE ("rotates over more degrees than");
+ RTYPE ("lincs-warnangle", ir->LincsWarnAngle, 30.0);
+ CTYPE ("Convert harmonic bonds to morse potentials");
+ EETYPE("morse", opts->bMorse, yesno_names);
+
+ /* Energy group exclusions */
+ CCTYPE ("ENERGY GROUP EXCLUSIONS");
+ CTYPE ("Pairs of energy groups for which all non-bonded interactions are excluded");
+ STYPE ("energygrp-excl", is->egpexcl, NULL);
+
+ /* Walls */
+ CCTYPE ("WALLS");
+ CTYPE ("Number of walls, type, atom types, densities and box-z scale factor for Ewald");
+ ITYPE ("nwall", ir->nwall, 0);
+ EETYPE("wall-type", ir->wall_type, ewt_names);
+ RTYPE ("wall-r-linpot", ir->wall_r_linpot, -1);
+ STYPE ("wall-atomtype", is->wall_atomtype, NULL);
+ STYPE ("wall-density", is->wall_density, NULL);
+ RTYPE ("wall-ewald-zfac", ir->wall_ewald_zfac, 3);
+
+ /* COM pulling */
+ CCTYPE("COM PULLING");
+ CTYPE("Pull type: no, umbrella, constraint or constant-force");
+ EETYPE("pull", ir->ePull, epull_names);
+ if (ir->ePull != epullNO)
+ {
+ snew(ir->pull, 1);
+ is->pull_grp = read_pullparams(&ninp, &inp, ir->pull, &opts->pull_start, wi);
+ }
+
+ /* Enforced rotation */
+ CCTYPE("ENFORCED ROTATION");
+ CTYPE("Enforced rotation: No or Yes");
+ EETYPE("rotation", ir->bRot, yesno_names);
+ if (ir->bRot)
+ {
+ snew(ir->rot, 1);
+ is->rot_grp = read_rotparams(&ninp, &inp, ir->rot, wi);
+ }
+
+ /* Interactive MD */
+ ir->bIMD = FALSE;
+ CCTYPE("Group to display and/or manipulate in interactive MD session");
+ STYPE ("IMD-group", is->imd_grp, NULL);
+ if (is->imd_grp[0] != '\0')
+ {
+ snew(ir->imd, 1);
+ ir->bIMD = TRUE;
+ }
+
+ /* Refinement */
+ CCTYPE("NMR refinement stuff");
+ CTYPE ("Distance restraints type: No, Simple or Ensemble");
+ EETYPE("disre", ir->eDisre, edisre_names);
+ CTYPE ("Force weighting of pairs in one distance restraint: Conservative or Equal");
+ EETYPE("disre-weighting", ir->eDisreWeighting, edisreweighting_names);
+ CTYPE ("Use sqrt of the time averaged times the instantaneous violation");
+ EETYPE("disre-mixed", ir->bDisreMixed, yesno_names);
+ RTYPE ("disre-fc", ir->dr_fc, 1000.0);
+ RTYPE ("disre-tau", ir->dr_tau, 0.0);
+ CTYPE ("Output frequency for pair distances to energy file");
+ ITYPE ("nstdisreout", ir->nstdisreout, 100);
+ CTYPE ("Orientation restraints: No or Yes");
+ EETYPE("orire", opts->bOrire, yesno_names);
+ CTYPE ("Orientation restraints force constant and tau for time averaging");
+ RTYPE ("orire-fc", ir->orires_fc, 0.0);
+ RTYPE ("orire-tau", ir->orires_tau, 0.0);
+ STYPE ("orire-fitgrp", is->orirefitgrp, NULL);
+ CTYPE ("Output frequency for trace(SD) and S to energy file");
+ ITYPE ("nstorireout", ir->nstorireout, 100);
+
+ /* free energy variables */
+ CCTYPE ("Free energy variables");
+ EETYPE("free-energy", ir->efep, efep_names);
+ STYPE ("couple-moltype", is->couple_moltype, NULL);
+ EETYPE("couple-lambda0", opts->couple_lam0, couple_lam);
+ EETYPE("couple-lambda1", opts->couple_lam1, couple_lam);
+ EETYPE("couple-intramol", opts->bCoupleIntra, yesno_names);
+
+ RTYPE ("init-lambda", fep->init_lambda, -1); /* start with -1 so
+ we can recognize if
+ it was not entered */
+ ITYPE ("init-lambda-state", fep->init_fep_state, -1);
+ RTYPE ("delta-lambda", fep->delta_lambda, 0.0);
+ ITYPE ("nstdhdl", fep->nstdhdl, 50);
+ STYPE ("fep-lambdas", is->fep_lambda[efptFEP], NULL);
+ STYPE ("mass-lambdas", is->fep_lambda[efptMASS], NULL);
+ STYPE ("coul-lambdas", is->fep_lambda[efptCOUL], NULL);
+ STYPE ("vdw-lambdas", is->fep_lambda[efptVDW], NULL);
+ STYPE ("bonded-lambdas", is->fep_lambda[efptBONDED], NULL);
+ STYPE ("restraint-lambdas", is->fep_lambda[efptRESTRAINT], NULL);
+ STYPE ("temperature-lambdas", is->fep_lambda[efptTEMPERATURE], NULL);
+ ITYPE ("calc-lambda-neighbors", fep->lambda_neighbors, 1);
+ STYPE ("init-lambda-weights", is->lambda_weights, NULL);
+ EETYPE("dhdl-print-energy", fep->bPrintEnergy, yesno_names);
+ RTYPE ("sc-alpha", fep->sc_alpha, 0.0);
+ ITYPE ("sc-power", fep->sc_power, 1);
+ RTYPE ("sc-r-power", fep->sc_r_power, 6.0);
+ RTYPE ("sc-sigma", fep->sc_sigma, 0.3);
+ EETYPE("sc-coul", fep->bScCoul, yesno_names);
+ ITYPE ("dh_hist_size", fep->dh_hist_size, 0);
+ RTYPE ("dh_hist_spacing", fep->dh_hist_spacing, 0.1);
+ EETYPE("separate-dhdl-file", fep->separate_dhdl_file,
+ separate_dhdl_file_names);
+ EETYPE("dhdl-derivatives", fep->dhdl_derivatives, dhdl_derivatives_names);
+ ITYPE ("dh_hist_size", fep->dh_hist_size, 0);
+ RTYPE ("dh_hist_spacing", fep->dh_hist_spacing, 0.1);
+
+ /* Non-equilibrium MD stuff */
+ CCTYPE("Non-equilibrium MD stuff");
+ STYPE ("acc-grps", is->accgrps, NULL);
+ STYPE ("accelerate", is->acc, NULL);
+ STYPE ("freezegrps", is->freeze, NULL);
+ STYPE ("freezedim", is->frdim, NULL);
+ RTYPE ("cos-acceleration", ir->cos_accel, 0);
+ STYPE ("deform", is->deform, NULL);
+
+ /* simulated tempering variables */
+ CCTYPE("simulated tempering variables");
+ EETYPE("simulated-tempering", ir->bSimTemp, yesno_names);
+ EETYPE("simulated-tempering-scaling", ir->simtempvals->eSimTempScale, esimtemp_names);
+ RTYPE("sim-temp-low", ir->simtempvals->simtemp_low, 300.0);
+ RTYPE("sim-temp-high", ir->simtempvals->simtemp_high, 300.0);
+
+ /* expanded ensemble variables */
+ if (ir->efep == efepEXPANDED || ir->bSimTemp)
+ {
+ read_expandedparams(&ninp, &inp, expand, wi);
+ }
+
+ /* Electric fields */
+ CCTYPE("Electric fields");
+ CTYPE ("Format is number of terms (int) and for all terms an amplitude (real)");
+ CTYPE ("and a phase angle (real)");
+ STYPE ("E-x", is->efield_x, NULL);
+ STYPE ("E-xt", is->efield_xt, NULL);
+ STYPE ("E-y", is->efield_y, NULL);
+ STYPE ("E-yt", is->efield_yt, NULL);
+ STYPE ("E-z", is->efield_z, NULL);
+ STYPE ("E-zt", is->efield_zt, NULL);
+
+ CCTYPE("Ion/water position swapping for computational electrophysiology setups");
+ CTYPE("Swap positions along direction: no, X, Y, Z");
+ EETYPE("swapcoords", ir->eSwapCoords, eSwapTypes_names);
+ if (ir->eSwapCoords != eswapNO)
+ {
+ snew(ir->swap, 1);
+ CTYPE("Swap attempt frequency");
+ ITYPE("swap-frequency", ir->swap->nstswap, 1);
+ CTYPE("Two index groups that contain the compartment-partitioning atoms");
+ STYPE("split-group0", splitgrp0, NULL);
+ STYPE("split-group1", splitgrp1, NULL);
+ CTYPE("Use center of mass of split groups (yes/no), otherwise center of geometry is used");
+ EETYPE("massw-split0", ir->swap->massw_split[0], yesno_names);
+ EETYPE("massw-split1", ir->swap->massw_split[1], yesno_names);
+
+ CTYPE("Group name of ions that can be exchanged with solvent molecules");
+ STYPE("swap-group", swapgrp, NULL);
+ CTYPE("Group name of solvent molecules");
+ STYPE("solvent-group", solgrp, NULL);
+
+ CTYPE("Split cylinder: radius, upper and lower extension (nm) (this will define the channels)");
+ CTYPE("Note that the split cylinder settings do not have an influence on the swapping protocol,");
+ CTYPE("however, if correctly defined, the ion permeation events are counted per channel");
+ RTYPE("cyl0-r", ir->swap->cyl0r, 2.0);
+ RTYPE("cyl0-up", ir->swap->cyl0u, 1.0);
+ RTYPE("cyl0-down", ir->swap->cyl0l, 1.0);
+ RTYPE("cyl1-r", ir->swap->cyl1r, 2.0);
+ RTYPE("cyl1-up", ir->swap->cyl1u, 1.0);
+ RTYPE("cyl1-down", ir->swap->cyl1l, 1.0);
+
+ CTYPE("Average the number of ions per compartment over these many swap attempt steps");
+ ITYPE("coupl-steps", ir->swap->nAverage, 10);
+ CTYPE("Requested number of anions and cations for each of the two compartments");
+ CTYPE("-1 means fix the numbers as found in time step 0");
+ ITYPE("anionsA", ir->swap->nanions[0], -1);
+ ITYPE("cationsA", ir->swap->ncations[0], -1);
+ ITYPE("anionsB", ir->swap->nanions[1], -1);
+ ITYPE("cationsB", ir->swap->ncations[1], -1);
+ CTYPE("Start to swap ions if threshold difference to requested count is reached");
+ RTYPE("threshold", ir->swap->threshold, 1.0);
+ }
+
+ /* AdResS defined thingies */
+ CCTYPE ("AdResS parameters");
+ EETYPE("adress", ir->bAdress, yesno_names);
+ if (ir->bAdress)
+ {
+ snew(ir->adress, 1);
+ read_adressparams(&ninp, &inp, ir->adress, wi);
+ }
+
+ /* User defined thingies */
+ CCTYPE ("User defined thingies");
+ STYPE ("user1-grps", is->user1, NULL);
+ STYPE ("user2-grps", is->user2, NULL);
+ ITYPE ("userint1", ir->userint1, 0);
+ ITYPE ("userint2", ir->userint2, 0);
+ ITYPE ("userint3", ir->userint3, 0);
+ ITYPE ("userint4", ir->userint4, 0);
+ RTYPE ("userreal1", ir->userreal1, 0);
+ RTYPE ("userreal2", ir->userreal2, 0);
+ RTYPE ("userreal3", ir->userreal3, 0);
+ RTYPE ("userreal4", ir->userreal4, 0);
+#undef CTYPE
+
+ write_inpfile(mdparout, ninp, inp, FALSE, wi);
+ for (i = 0; (i < ninp); i++)
+ {
+ sfree(inp[i].name);
+ sfree(inp[i].value);
+ }
+ sfree(inp);
+
+ /* Process options if necessary */
+ for (m = 0; m < 2; m++)
+ {
+ for (i = 0; i < 2*DIM; i++)
+ {
+ dumdub[m][i] = 0.0;
+ }
+ if (ir->epc)
+ {
+ switch (ir->epct)
+ {
+ case epctISOTROPIC:
+ if (sscanf(dumstr[m], "%lf", &(dumdub[m][XX])) != 1)
+ {
+ warning_error(wi, "Pressure coupling not enough values (I need 1)");
+ }
+ dumdub[m][YY] = dumdub[m][ZZ] = dumdub[m][XX];
+ break;
+ case epctSEMIISOTROPIC:
+ case epctSURFACETENSION:
+ if (sscanf(dumstr[m], "%lf%lf",
+ &(dumdub[m][XX]), &(dumdub[m][ZZ])) != 2)
+ {
+ warning_error(wi, "Pressure coupling not enough values (I need 2)");
+ }
+ dumdub[m][YY] = dumdub[m][XX];
+ break;
+ case epctANISOTROPIC:
+ if (sscanf(dumstr[m], "%lf%lf%lf%lf%lf%lf",
+ &(dumdub[m][XX]), &(dumdub[m][YY]), &(dumdub[m][ZZ]),
+ &(dumdub[m][3]), &(dumdub[m][4]), &(dumdub[m][5])) != 6)
+ {
+ warning_error(wi, "Pressure coupling not enough values (I need 6)");
+ }
+ break;
+ default:
+ gmx_fatal(FARGS, "Pressure coupling type %s not implemented yet",
+ epcoupltype_names[ir->epct]);
+ }
+ }
+ }
+ clear_mat(ir->ref_p);
+ clear_mat(ir->compress);
+ for (i = 0; i < DIM; i++)
+ {
+ ir->ref_p[i][i] = dumdub[1][i];
+ ir->compress[i][i] = dumdub[0][i];
+ }
+ if (ir->epct == epctANISOTROPIC)
+ {
+ ir->ref_p[XX][YY] = dumdub[1][3];
+ ir->ref_p[XX][ZZ] = dumdub[1][4];
+ ir->ref_p[YY][ZZ] = dumdub[1][5];
+ if (ir->ref_p[XX][YY] != 0 && ir->ref_p[XX][ZZ] != 0 && ir->ref_p[YY][ZZ] != 0)
+ {
+ warning(wi, "All off-diagonal reference pressures are non-zero. Are you sure you want to apply a threefold shear stress?\n");
+ }
+ ir->compress[XX][YY] = dumdub[0][3];
+ ir->compress[XX][ZZ] = dumdub[0][4];
+ ir->compress[YY][ZZ] = dumdub[0][5];
+ for (i = 0; i < DIM; i++)
+ {
+ for (m = 0; m < i; m++)
+ {
+ ir->ref_p[i][m] = ir->ref_p[m][i];
+ ir->compress[i][m] = ir->compress[m][i];
+ }
+ }
+ }
+
+ if (ir->comm_mode == ecmNO)
+ {
+ ir->nstcomm = 0;
+ }
+
+ opts->couple_moltype = NULL;
+ if (strlen(is->couple_moltype) > 0)
+ {
+ if (ir->efep != efepNO)
+ {
+ opts->couple_moltype = strdup(is->couple_moltype);
+ if (opts->couple_lam0 == opts->couple_lam1)
+ {
+ warning(wi, "The lambda=0 and lambda=1 states for coupling are identical");
+ }
+ if (ir->eI == eiMD && (opts->couple_lam0 == ecouplamNONE ||
+ opts->couple_lam1 == ecouplamNONE))
+ {
+ warning(wi, "For proper sampling of the (nearly) decoupled state, stochastic dynamics should be used");
+ }
+ }
+ else
+ {
+ warning(wi, "Can not couple a molecule with free_energy = no");
+ }
+ }
+ /* FREE ENERGY AND EXPANDED ENSEMBLE OPTIONS */
+ if (ir->efep != efepNO)
+ {
+ if (fep->delta_lambda > 0)
+ {
+ ir->efep = efepSLOWGROWTH;
+ }
+ }
+
+ if (ir->bSimTemp)
+ {
+ fep->bPrintEnergy = TRUE;
+ /* always print out the energy to dhdl if we are doing expanded ensemble, since we need the total energy
+ if the temperature is changing. */
+ }
+
+ if ((ir->efep != efepNO) || ir->bSimTemp)
+ {
+ ir->bExpanded = FALSE;
+ if ((ir->efep == efepEXPANDED) || ir->bSimTemp)
+ {
+ ir->bExpanded = TRUE;
+ }
+ do_fep_params(ir, is->fep_lambda, is->lambda_weights);
+ if (ir->bSimTemp) /* done after fep params */
+ {
+ do_simtemp_params(ir);
+ }
+ }
+ else
+ {
+ ir->fepvals->n_lambda = 0;
+ }
+
+ /* WALL PARAMETERS */
+
+ do_wall_params(ir, is->wall_atomtype, is->wall_density, opts);
+
+ /* ORIENTATION RESTRAINT PARAMETERS */
+
+ if (opts->bOrire && str_nelem(is->orirefitgrp, MAXPTR, NULL) != 1)
+ {
+ warning_error(wi, "ERROR: Need one orientation restraint fit group\n");
+ }
+
+ /* DEFORMATION PARAMETERS */
+
+ clear_mat(ir->deform);
+ for (i = 0; i < 6; i++)
+ {
+ dumdub[0][i] = 0;
+ }
+ m = sscanf(is->deform, "%lf %lf %lf %lf %lf %lf",
+ &(dumdub[0][0]), &(dumdub[0][1]), &(dumdub[0][2]),
+ &(dumdub[0][3]), &(dumdub[0][4]), &(dumdub[0][5]));
+ for (i = 0; i < 3; i++)
+ {
+ ir->deform[i][i] = dumdub[0][i];
+ }
+ ir->deform[YY][XX] = dumdub[0][3];
+ ir->deform[ZZ][XX] = dumdub[0][4];
+ ir->deform[ZZ][YY] = dumdub[0][5];
+ if (ir->epc != epcNO)
+ {
+ for (i = 0; i < 3; i++)
+ {
+ for (j = 0; j <= i; j++)
+ {
+ if (ir->deform[i][j] != 0 && ir->compress[i][j] != 0)
+ {
+ warning_error(wi, "A box element has deform set and compressibility > 0");
+ }
+ }
+ }
+ for (i = 0; i < 3; i++)
+ {
+ for (j = 0; j < i; j++)
+ {
+ if (ir->deform[i][j] != 0)
+ {
+ for (m = j; m < DIM; m++)
+ {
+ if (ir->compress[m][j] != 0)
+ {
+ sprintf(warn_buf, "An off-diagonal box element has deform set while compressibility > 0 for the same component of another box vector, this might lead to spurious periodicity effects.");
+ warning(wi, warn_buf);
+ }
+ }
+ }
+ }
+ }
+ }
+
+ /* Ion/water position swapping checks */
+ if (ir->eSwapCoords != eswapNO)
+ {
+ if (ir->swap->nstswap < 1)
+ {
+ warning_error(wi, "swap_frequency must be 1 or larger when ion swapping is requested");
+ }
+ if (ir->swap->nAverage < 1)
+ {
+ warning_error(wi, "coupl_steps must be 1 or larger.\n");
+ }
+ if (ir->swap->threshold < 1.0)
+ {
+ warning_error(wi, "Ion count threshold must be at least 1.\n");
+ }
+ }
+
+ sfree(dumstr[0]);
+ sfree(dumstr[1]);
+}
+
+static int search_QMstring(const char *s, int ng, const char *gn[])
+{
+ /* same as normal search_string, but this one searches QM strings */
+ int i;
+
+ for (i = 0; (i < ng); i++)
+ {
+ if (gmx_strcasecmp(s, gn[i]) == 0)
+ {
+ return i;
+ }
+ }
+
+ gmx_fatal(FARGS, "this QM method or basisset (%s) is not implemented\n!", s);
+
+ return -1;
+
+} /* search_QMstring */
+
+/* We would like gn to be const as well, but C doesn't allow this */
+int search_string(const char *s, int ng, char *gn[])
+{
+ int i;
+
+ for (i = 0; (i < ng); i++)
+ {
+ if (gmx_strcasecmp(s, gn[i]) == 0)
+ {
+ return i;
+ }
+ }
+
+ gmx_fatal(FARGS,
+ "Group %s referenced in the .mdp file was not found in the index file.\n"
+ "Group names must match either [moleculetype] names or custom index group\n"
+ "names, in which case you must supply an index file to the '-n' option\n"
+ "of grompp.",
+ s);
+
+ return -1;
+}
+
+static gmx_bool do_numbering(int natoms, gmx_groups_t *groups, int ng, char *ptrs[],
+ t_blocka *block, char *gnames[],
+ int gtype, int restnm,
+ int grptp, gmx_bool bVerbose,
+ warninp_t wi)
+{
+ unsigned short *cbuf;
+ t_grps *grps = &(groups->grps[gtype]);
+ int i, j, gid, aj, ognr, ntot = 0;
+ const char *title;
+ gmx_bool bRest;
+ char warn_buf[STRLEN];
+
+ if (debug)
+ {
+ fprintf(debug, "Starting numbering %d groups of type %d\n", ng, gtype);
+ }
+
+ title = gtypes[gtype];
+
+ snew(cbuf, natoms);
+ /* Mark all id's as not set */
+ for (i = 0; (i < natoms); i++)
+ {
+ cbuf[i] = NOGID;
+ }
+
+ snew(grps->nm_ind, ng+1); /* +1 for possible rest group */
+ for (i = 0; (i < ng); i++)
+ {
+ /* Lookup the group name in the block structure */
+ gid = search_string(ptrs[i], block->nr, gnames);
+ if ((grptp != egrptpONE) || (i == 0))
+ {
+ grps->nm_ind[grps->nr++] = gid;
+ }
+ if (debug)
+ {
+ fprintf(debug, "Found gid %d for group %s\n", gid, ptrs[i]);
+ }
+
+ /* Now go over the atoms in the group */
+ for (j = block->index[gid]; (j < block->index[gid+1]); j++)
+ {
+
+ aj = block->a[j];
+
+ /* Range checking */
+ if ((aj < 0) || (aj >= natoms))
+ {
+ gmx_fatal(FARGS, "Invalid atom number %d in indexfile", aj);
+ }
+ /* Lookup up the old group number */
+ ognr = cbuf[aj];
+ if (ognr != NOGID)
+ {
+ gmx_fatal(FARGS, "Atom %d in multiple %s groups (%d and %d)",
+ aj+1, title, ognr+1, i+1);
+ }
+ else
+ {
+ /* Store the group number in buffer */
+ if (grptp == egrptpONE)
+ {
+ cbuf[aj] = 0;
+ }
+ else
+ {
+ cbuf[aj] = i;
+ }
+ ntot++;
+ }
+ }
+ }
+
+ /* Now check whether we have done all atoms */
+ bRest = FALSE;
+ if (ntot != natoms)
+ {
+ if (grptp == egrptpALL)
+ {
+ gmx_fatal(FARGS, "%d atoms are not part of any of the %s groups",
+ natoms-ntot, title);
+ }
+ else if (grptp == egrptpPART)
+ {
+ sprintf(warn_buf, "%d atoms are not part of any of the %s groups",
+ natoms-ntot, title);
+ warning_note(wi, warn_buf);
+ }
+ /* Assign all atoms currently unassigned to a rest group */
+ for (j = 0; (j < natoms); j++)
+ {
+ if (cbuf[j] == NOGID)
+ {
+ cbuf[j] = grps->nr;
+ bRest = TRUE;
+ }
+ }
+ if (grptp != egrptpPART)
+ {
+ if (bVerbose)
+ {
+ fprintf(stderr,
+ "Making dummy/rest group for %s containing %d elements\n",
+ title, natoms-ntot);
+ }
+ /* Add group name "rest" */
+ grps->nm_ind[grps->nr] = restnm;
+
+ /* Assign the rest name to all atoms not currently assigned to a group */
+ for (j = 0; (j < natoms); j++)
+ {
+ if (cbuf[j] == NOGID)
+ {
+ cbuf[j] = grps->nr;
+ }
+ }
+ grps->nr++;
+ }
+ }
+
+ if (grps->nr == 1 && (ntot == 0 || ntot == natoms))
+ {
+ /* All atoms are part of one (or no) group, no index required */
+ groups->ngrpnr[gtype] = 0;
+ groups->grpnr[gtype] = NULL;
+ }
+ else
+ {
+ groups->ngrpnr[gtype] = natoms;
+ snew(groups->grpnr[gtype], natoms);
+ for (j = 0; (j < natoms); j++)
+ {
+ groups->grpnr[gtype][j] = cbuf[j];
+ }
+ }
+
+ sfree(cbuf);
+
+ return (bRest && grptp == egrptpPART);
+}
+
+static void calc_nrdf(gmx_mtop_t *mtop, t_inputrec *ir, char **gnames)
+{
+ t_grpopts *opts;
+ gmx_groups_t *groups;
+ t_pull *pull;
+ int natoms, ai, aj, i, j, d, g, imin, jmin;
+ t_iatom *ia;
+ int *nrdf2, *na_vcm, na_tot;
+ double *nrdf_tc, *nrdf_vcm, nrdf_uc, n_sub = 0;
+ gmx_mtop_atomloop_all_t aloop;
+ t_atom *atom;
+ int mb, mol, ftype, as;
+ gmx_molblock_t *molb;
+ gmx_moltype_t *molt;
+
+ /* Calculate nrdf.
+ * First calc 3xnr-atoms for each group
+ * then subtract half a degree of freedom for each constraint
+ *
+ * Only atoms and nuclei contribute to the degrees of freedom...
+ */
+
+ opts = &ir->opts;
+
+ groups = &mtop->groups;
+ natoms = mtop->natoms;
+
+ /* Allocate one more for a possible rest group */
+ /* We need to sum degrees of freedom into doubles,
+ * since floats give too low nrdf's above 3 million atoms.
+ */
+ snew(nrdf_tc, groups->grps[egcTC].nr+1);
+ snew(nrdf_vcm, groups->grps[egcVCM].nr+1);
+ snew(na_vcm, groups->grps[egcVCM].nr+1);
+
+ for (i = 0; i < groups->grps[egcTC].nr; i++)
+ {
+ nrdf_tc[i] = 0;
+ }
+ for (i = 0; i < groups->grps[egcVCM].nr+1; i++)
+ {
+ nrdf_vcm[i] = 0;
+ }
+
+ snew(nrdf2, natoms);
+ aloop = gmx_mtop_atomloop_all_init(mtop);
+ while (gmx_mtop_atomloop_all_next(aloop, &i, &atom))
+ {
+ nrdf2[i] = 0;
+ if (atom->ptype == eptAtom || atom->ptype == eptNucleus)
+ {
+ g = ggrpnr(groups, egcFREEZE, i);
+ /* Double count nrdf for particle i */
+ for (d = 0; d < DIM; d++)
+ {
+ if (opts->nFreeze[g][d] == 0)
+ {
+ nrdf2[i] += 2;
+ }
+ }
+ nrdf_tc [ggrpnr(groups, egcTC, i)] += 0.5*nrdf2[i];
+ nrdf_vcm[ggrpnr(groups, egcVCM, i)] += 0.5*nrdf2[i];
+ }
+ }
+
+ as = 0;
+ for (mb = 0; mb < mtop->nmolblock; mb++)
+ {
+ molb = &mtop->molblock[mb];
+ molt = &mtop->moltype[molb->type];
+ atom = molt->atoms.atom;
+ for (mol = 0; mol < molb->nmol; mol++)
+ {
+ for (ftype = F_CONSTR; ftype <= F_CONSTRNC; ftype++)
+ {
+ ia = molt->ilist[ftype].iatoms;
+ for (i = 0; i < molt->ilist[ftype].nr; )
+ {
+ /* Subtract degrees of freedom for the constraints,
+ * if the particles still have degrees of freedom left.
+ * If one of the particles is a vsite or a shell, then all
+ * constraint motion will go there, but since they do not
+ * contribute to the constraints the degrees of freedom do not
+ * change.
+ */
+ ai = as + ia[1];
+ aj = as + ia[2];
+ if (((atom[ia[1]].ptype == eptNucleus) ||
+ (atom[ia[1]].ptype == eptAtom)) &&
+ ((atom[ia[2]].ptype == eptNucleus) ||
+ (atom[ia[2]].ptype == eptAtom)))
+ {
+ if (nrdf2[ai] > 0)
+ {
+ jmin = 1;
+ }
+ else
+ {
+ jmin = 2;
+ }
+ if (nrdf2[aj] > 0)
+ {
+ imin = 1;
+ }
+ else
+ {
+ imin = 2;
+ }
+ imin = min(imin, nrdf2[ai]);
+ jmin = min(jmin, nrdf2[aj]);
+ nrdf2[ai] -= imin;
+ nrdf2[aj] -= jmin;
+ nrdf_tc [ggrpnr(groups, egcTC, ai)] -= 0.5*imin;
+ nrdf_tc [ggrpnr(groups, egcTC, aj)] -= 0.5*jmin;
+ nrdf_vcm[ggrpnr(groups, egcVCM, ai)] -= 0.5*imin;
+ nrdf_vcm[ggrpnr(groups, egcVCM, aj)] -= 0.5*jmin;
+ }
+ ia += interaction_function[ftype].nratoms+1;
+ i += interaction_function[ftype].nratoms+1;
+ }
+ }
+ ia = molt->ilist[F_SETTLE].iatoms;
+ for (i = 0; i < molt->ilist[F_SETTLE].nr; )
+ {
+ /* Subtract 1 dof from every atom in the SETTLE */
+ for (j = 0; j < 3; j++)
+ {
+ ai = as + ia[1+j];
+ imin = min(2, nrdf2[ai]);
+ nrdf2[ai] -= imin;
+ nrdf_tc [ggrpnr(groups, egcTC, ai)] -= 0.5*imin;
+ nrdf_vcm[ggrpnr(groups, egcVCM, ai)] -= 0.5*imin;
+ }
+ ia += 4;
+ i += 4;
+ }
+ as += molt->atoms.nr;
+ }
+ }
+
+ if (ir->ePull == epullCONSTRAINT)
+ {
+ /* Correct nrdf for the COM constraints.
+ * We correct using the TC and VCM group of the first atom
+ * in the reference and pull group. If atoms in one pull group
+ * belong to different TC or VCM groups it is anyhow difficult
+ * to determine the optimal nrdf assignment.
+ */
+ pull = ir->pull;
+
+ for (i = 0; i < pull->ncoord; i++)
+ {
+ imin = 1;
+
+ for (j = 0; j < 2; j++)
+ {
+ const t_pull_group *pgrp;
+
+ pgrp = &pull->group[pull->coord[i].group[j]];
+
+ if (pgrp->nat > 0)
+ {
+ /* Subtract 1/2 dof from each group */
+ ai = pgrp->ind[0];
+ nrdf_tc [ggrpnr(groups, egcTC, ai)] -= 0.5*imin;
+ nrdf_vcm[ggrpnr(groups, egcVCM, ai)] -= 0.5*imin;
+ if (nrdf_tc[ggrpnr(groups, egcTC, ai)] < 0)
+ {
+ gmx_fatal(FARGS, "Center of mass pulling constraints caused the number of degrees of freedom for temperature coupling group %s to be negative", gnames[groups->grps[egcTC].nm_ind[ggrpnr(groups, egcTC, ai)]]);
+ }
+ }
+ else
+ {
+ /* We need to subtract the whole DOF from group j=1 */
+ imin += 1;
+ }
+ }
+ }
+ }
+
+ if (ir->nstcomm != 0)
+ {
+ /* Subtract 3 from the number of degrees of freedom in each vcm group
+ * when com translation is removed and 6 when rotation is removed
+ * as well.
+ */
+ switch (ir->comm_mode)
+ {
+ case ecmLINEAR:
+ n_sub = ndof_com(ir);
+ break;
+ case ecmANGULAR:
+ n_sub = 6;
+ break;
+ default:
+ n_sub = 0;
+ gmx_incons("Checking comm_mode");
+ }
+
+ for (i = 0; i < groups->grps[egcTC].nr; i++)
+ {
+ /* Count the number of atoms of TC group i for every VCM group */
+ for (j = 0; j < groups->grps[egcVCM].nr+1; j++)
+ {
+ na_vcm[j] = 0;
+ }
+ na_tot = 0;
+ for (ai = 0; ai < natoms; ai++)
+ {
+ if (ggrpnr(groups, egcTC, ai) == i)
+ {
+ na_vcm[ggrpnr(groups, egcVCM, ai)]++;
+ na_tot++;
+ }
+ }
+ /* Correct for VCM removal according to the fraction of each VCM
+ * group present in this TC group.
+ */
+ nrdf_uc = nrdf_tc[i];
+ if (debug)
+ {
+ fprintf(debug, "T-group[%d] nrdf_uc = %g, n_sub = %g\n",
+ i, nrdf_uc, n_sub);
+ }
+ nrdf_tc[i] = 0;
+ for (j = 0; j < groups->grps[egcVCM].nr+1; j++)
+ {
+ if (nrdf_vcm[j] > n_sub)
+ {
+ nrdf_tc[i] += nrdf_uc*((double)na_vcm[j]/(double)na_tot)*
+ (nrdf_vcm[j] - n_sub)/nrdf_vcm[j];
+ }
+ if (debug)
+ {
+ fprintf(debug, " nrdf_vcm[%d] = %g, nrdf = %g\n",
+ j, nrdf_vcm[j], nrdf_tc[i]);
+ }
+ }
+ }
+ }
+ for (i = 0; (i < groups->grps[egcTC].nr); i++)
+ {
+ opts->nrdf[i] = nrdf_tc[i];
+ if (opts->nrdf[i] < 0)
+ {
+ opts->nrdf[i] = 0;
+ }
+ fprintf(stderr,
+ "Number of degrees of freedom in T-Coupling group %s is %.2f\n",
+ gnames[groups->grps[egcTC].nm_ind[i]], opts->nrdf[i]);
+ }
+
+ sfree(nrdf2);
+ sfree(nrdf_tc);
+ sfree(nrdf_vcm);
+ sfree(na_vcm);
+}
+
+static void decode_cos(char *s, t_cosines *cosine)
+{
+ char *t;
+ char format[STRLEN], f1[STRLEN];
+ double a, phi;
+ int i;
+
+ t = strdup(s);
+ trim(t);
+
+ cosine->n = 0;
+ cosine->a = NULL;
+ cosine->phi = NULL;
+ if (strlen(t))
+ {
+ sscanf(t, "%d", &(cosine->n));
+ if (cosine->n <= 0)
+ {
+ cosine->n = 0;
+ }
+ else
+ {
+ snew(cosine->a, cosine->n);
+ snew(cosine->phi, cosine->n);
+
+ sprintf(format, "%%*d");
+ for (i = 0; (i < cosine->n); i++)
+ {
+ strcpy(f1, format);
+ strcat(f1, "%lf%lf");
+ if (sscanf(t, f1, &a, &phi) < 2)
+ {
+ gmx_fatal(FARGS, "Invalid input for electric field shift: '%s'", t);
+ }
+ cosine->a[i] = a;
+ cosine->phi[i] = phi;
+ strcat(format, "%*lf%*lf");
+ }
+ }
+ }
+ sfree(t);
+}
+
+static gmx_bool do_egp_flag(t_inputrec *ir, gmx_groups_t *groups,
+ const char *option, const char *val, int flag)
+{
+ /* The maximum number of energy group pairs would be MAXPTR*(MAXPTR+1)/2.
+ * But since this is much larger than STRLEN, such a line can not be parsed.
+ * The real maximum is the number of names that fit in a string: STRLEN/2.
+ */
+#define EGP_MAX (STRLEN/2)
+ int nelem, i, j, k, nr;
+ char *names[EGP_MAX];
+ char ***gnames;
+ gmx_bool bSet;
+
+ gnames = groups->grpname;
+
+ nelem = str_nelem(val, EGP_MAX, names);
+ if (nelem % 2 != 0)
+ {
+ gmx_fatal(FARGS, "The number of groups for %s is odd", option);
+ }
+ nr = groups->grps[egcENER].nr;
+ bSet = FALSE;
+ for (i = 0; i < nelem/2; i++)
+ {
+ j = 0;
+ while ((j < nr) &&
+ gmx_strcasecmp(names[2*i], *(gnames[groups->grps[egcENER].nm_ind[j]])))
+ {
+ j++;
+ }
+ if (j == nr)
+ {
+ gmx_fatal(FARGS, "%s in %s is not an energy group\n",
+ names[2*i], option);
+ }
+ k = 0;
+ while ((k < nr) &&
+ gmx_strcasecmp(names[2*i+1], *(gnames[groups->grps[egcENER].nm_ind[k]])))
+ {
+ k++;
+ }
+ if (k == nr)
+ {
+ gmx_fatal(FARGS, "%s in %s is not an energy group\n",
+ names[2*i+1], option);
+ }
+ if ((j < nr) && (k < nr))
+ {
+ ir->opts.egp_flags[nr*j+k] |= flag;
+ ir->opts.egp_flags[nr*k+j] |= flag;
+ bSet = TRUE;
+ }
+ }
+
+ return bSet;
+}
+
+
+static void make_swap_groups(
+ t_swapcoords *swap,
+ char *swapgname,
+ char *splitg0name,
+ char *splitg1name,
+ char *solgname,
+ t_blocka *grps,
+ char **gnames)
+{
+ int ig = -1, i = 0, j;
+ char *splitg;
+
+
+ /* Just a quick check here, more thorough checks are in mdrun */
+ if (strcmp(splitg0name, splitg1name) == 0)
+ {
+ gmx_fatal(FARGS, "The split groups can not both be '%s'.", splitg0name);
+ }
+
+ /* First get the swap group index atoms */
+ ig = search_string(swapgname, grps->nr, gnames);
+ swap->nat = grps->index[ig+1] - grps->index[ig];
+ if (swap->nat > 0)
+ {
+ fprintf(stderr, "Swap group '%s' contains %d atoms.\n", swapgname, swap->nat);
+ snew(swap->ind, swap->nat);
+ for (i = 0; i < swap->nat; i++)
+ {
+ swap->ind[i] = grps->a[grps->index[ig]+i];
+ }
+ }
+ else
+ {
+ gmx_fatal(FARGS, "You defined an empty group of atoms for swapping.");
+ }
+
+ /* Now do so for the split groups */
+ for (j = 0; j < 2; j++)
+ {
+ if (j == 0)
+ {
+ splitg = splitg0name;
+ }
+ else
+ {
+ splitg = splitg1name;
+ }
+
+ ig = search_string(splitg, grps->nr, gnames);
+ swap->nat_split[j] = grps->index[ig+1] - grps->index[ig];
+ if (swap->nat_split[j] > 0)
+ {
+ fprintf(stderr, "Split group %d '%s' contains %d atom%s.\n",
+ j, splitg, swap->nat_split[j], (swap->nat_split[j] > 1) ? "s" : "");
+ snew(swap->ind_split[j], swap->nat_split[j]);
+ for (i = 0; i < swap->nat_split[j]; i++)
+ {
+ swap->ind_split[j][i] = grps->a[grps->index[ig]+i];
+ }
+ }
+ else
+ {
+ gmx_fatal(FARGS, "Split group %d has to contain at least 1 atom!", j);
+ }
+ }
+
+ /* Now get the solvent group index atoms */
+ ig = search_string(solgname, grps->nr, gnames);
+ swap->nat_sol = grps->index[ig+1] - grps->index[ig];
+ if (swap->nat_sol > 0)
+ {
+ fprintf(stderr, "Solvent group '%s' contains %d atoms.\n", solgname, swap->nat_sol);
+ snew(swap->ind_sol, swap->nat_sol);
+ for (i = 0; i < swap->nat_sol; i++)
+ {
+ swap->ind_sol[i] = grps->a[grps->index[ig]+i];
+ }
+ }
+ else
+ {
+ gmx_fatal(FARGS, "You defined an empty group of solvent. Cannot exchange ions.");
+ }
+}
+
+
+void make_IMD_group(t_IMD *IMDgroup, char *IMDgname, t_blocka *grps, char **gnames)
+{
+ int ig = -1, i;
+
+
+ ig = search_string(IMDgname, grps->nr, gnames);
+ IMDgroup->nat = grps->index[ig+1] - grps->index[ig];
+
+ if (IMDgroup->nat > 0)
+ {
+ fprintf(stderr, "Group '%s' with %d atoms can be activated for interactive molecular dynamics (IMD).\n",
+ IMDgname, IMDgroup->nat);
+ snew(IMDgroup->ind, IMDgroup->nat);
+ for (i = 0; i < IMDgroup->nat; i++)
+ {
+ IMDgroup->ind[i] = grps->a[grps->index[ig]+i];
+ }
+ }
+}
+
+
+void do_index(const char* mdparin, const char *ndx,
+ gmx_mtop_t *mtop,
+ gmx_bool bVerbose,
+ t_inputrec *ir, rvec *v,
+ warninp_t wi)
+{
+ t_blocka *grps;
+ gmx_groups_t *groups;
+ int natoms;
+ t_symtab *symtab;
+ t_atoms atoms_all;
+ char warnbuf[STRLEN], **gnames;
+ int nr, ntcg, ntau_t, nref_t, nacc, nofg, nSA, nSA_points, nSA_time, nSA_temp;
+ real tau_min;
+ int nstcmin;
+ int nacg, nfreeze, nfrdim, nenergy, nvcm, nuser;
+ char *ptr1[MAXPTR], *ptr2[MAXPTR], *ptr3[MAXPTR];
+ int i, j, k, restnm;
+ real SAtime;
+ gmx_bool bExcl, bTable, bSetTCpar, bAnneal, bRest;
+ int nQMmethod, nQMbasis, nQMcharge, nQMmult, nbSH, nCASorb, nCASelec,
+ nSAon, nSAoff, nSAsteps, nQMg, nbOPT, nbTS;
+ char warn_buf[STRLEN];
+
+ if (bVerbose)
+ {
+ fprintf(stderr, "processing index file...\n");
+ }
+ debug_gmx();
+ if (ndx == NULL)
+ {
+ snew(grps, 1);
+ snew(grps->index, 1);
+ snew(gnames, 1);
+ atoms_all = gmx_mtop_global_atoms(mtop);
+ analyse(&atoms_all, grps, &gnames, FALSE, TRUE);
+ free_t_atoms(&atoms_all, FALSE);
+ }
+ else
+ {
+ grps = init_index(ndx, &gnames);
+ }
+
+ groups = &mtop->groups;
+ natoms = mtop->natoms;
+ symtab = &mtop->symtab;
+
+ snew(groups->grpname, grps->nr+1);
+
+ for (i = 0; (i < grps->nr); i++)
+ {
+ groups->grpname[i] = put_symtab(symtab, gnames[i]);
+ }
+ groups->grpname[i] = put_symtab(symtab, "rest");
+ restnm = i;
+ srenew(gnames, grps->nr+1);
+ gnames[restnm] = *(groups->grpname[i]);
+ groups->ngrpname = grps->nr+1;
+
+ set_warning_line(wi, mdparin, -1);
+
+ ntau_t = str_nelem(is->tau_t, MAXPTR, ptr1);
+ nref_t = str_nelem(is->ref_t, MAXPTR, ptr2);
+ ntcg = str_nelem(is->tcgrps, MAXPTR, ptr3);
+ if ((ntau_t != ntcg) || (nref_t != ntcg))
+ {
+ gmx_fatal(FARGS, "Invalid T coupling input: %d groups, %d ref-t values and "
+ "%d tau-t values", ntcg, nref_t, ntau_t);
+ }
+
+ bSetTCpar = (ir->etc || EI_SD(ir->eI) || ir->eI == eiBD || EI_TPI(ir->eI));
+ do_numbering(natoms, groups, ntcg, ptr3, grps, gnames, egcTC,
+ restnm, bSetTCpar ? egrptpALL : egrptpALL_GENREST, bVerbose, wi);
+ nr = groups->grps[egcTC].nr;
+ ir->opts.ngtc = nr;
+ snew(ir->opts.nrdf, nr);
+ snew(ir->opts.tau_t, nr);
+ snew(ir->opts.ref_t, nr);
+ if (ir->eI == eiBD && ir->bd_fric == 0)
+ {
+ fprintf(stderr, "bd-fric=0, so tau-t will be used as the inverse friction constant(s)\n");
+ }
+
+ if (bSetTCpar)
+ {
+ if (nr != nref_t)
+ {
+ gmx_fatal(FARGS, "Not enough ref-t and tau-t values!");
+ }
+
+ tau_min = 1e20;
+ for (i = 0; (i < nr); i++)
+ {
+ ir->opts.tau_t[i] = strtod(ptr1[i], NULL);
+ if ((ir->eI == eiBD || ir->eI == eiSD2) && ir->opts.tau_t[i] <= 0)
+ {
+ sprintf(warn_buf, "With integrator %s tau-t should be larger than 0", ei_names[ir->eI]);
+ warning_error(wi, warn_buf);
+ }
+
+ if (ir->etc != etcVRESCALE && ir->opts.tau_t[i] == 0)
+ {
+ warning_note(wi, "tau-t = -1 is the value to signal that a group should not have temperature coupling. Treating your use of tau-t = 0 as if you used -1.");
+ }
+
+ if (ir->opts.tau_t[i] >= 0)
+ {
+ tau_min = min(tau_min, ir->opts.tau_t[i]);
+ }
+ }
+ if (ir->etc != etcNO && ir->nsttcouple == -1)
+ {
+ ir->nsttcouple = ir_optimal_nsttcouple(ir);
+ }
+
+ if (EI_VV(ir->eI))
+ {
+ if ((ir->etc == etcNOSEHOOVER) && (ir->epc == epcBERENDSEN))
+ {
+ gmx_fatal(FARGS, "Cannot do Nose-Hoover temperature with Berendsen pressure control with md-vv; use either vrescale temperature with berendsen pressure or Nose-Hoover temperature with MTTK pressure");
+ }
+ if ((ir->epc == epcMTTK) && (ir->etc > etcNO))
+ {
+ if (ir->nstpcouple != ir->nsttcouple)
+ {
+ int mincouple = min(ir->nstpcouple, ir->nsttcouple);
+ ir->nstpcouple = ir->nsttcouple = mincouple;
+ sprintf(warn_buf, "for current Trotter decomposition methods with vv, nsttcouple and nstpcouple must be equal. Both have been reset to min(nsttcouple,nstpcouple) = %d", mincouple);
+ warning_note(wi, warn_buf);
+ }
+ }
+ }
+ /* velocity verlet with averaged kinetic energy KE = 0.5*(v(t+1/2) - v(t-1/2)) is implemented
+ primarily for testing purposes, and does not work with temperature coupling other than 1 */
+
+ if (ETC_ANDERSEN(ir->etc))
+ {
+ if (ir->nsttcouple != 1)
+ {
+ ir->nsttcouple = 1;
+ sprintf(warn_buf, "Andersen temperature control methods assume nsttcouple = 1; there is no need for larger nsttcouple > 1, since no global parameters are computed. nsttcouple has been reset to 1");
+ warning_note(wi, warn_buf);
+ }
+ }
+ nstcmin = tcouple_min_integration_steps(ir->etc);
+ if (nstcmin > 1)
+ {
+ if (tau_min/(ir->delta_t*ir->nsttcouple) < nstcmin)
+ {
+ sprintf(warn_buf, "For proper integration of the %s thermostat, tau-t (%g) should be at least %d times larger than nsttcouple*dt (%g)",
+ ETCOUPLTYPE(ir->etc),
+ tau_min, nstcmin,
+ ir->nsttcouple*ir->delta_t);
+ warning(wi, warn_buf);
+ }
+ }
+ for (i = 0; (i < nr); i++)
+ {
+ ir->opts.ref_t[i] = strtod(ptr2[i], NULL);
+ if (ir->opts.ref_t[i] < 0)
+ {
+ gmx_fatal(FARGS, "ref-t for group %d negative", i);
+ }
+ }
+ /* set the lambda mc temperature to the md integrator temperature (which should be defined
+ if we are in this conditional) if mc_temp is negative */
+ if (ir->expandedvals->mc_temp < 0)
+ {
+ ir->expandedvals->mc_temp = ir->opts.ref_t[0]; /*for now, set to the first reft */
+ }
+ }
+
+ /* Simulated annealing for each group. There are nr groups */
+ nSA = str_nelem(is->anneal, MAXPTR, ptr1);
+ if (nSA == 1 && (ptr1[0][0] == 'n' || ptr1[0][0] == 'N'))
+ {
+ nSA = 0;
+ }
+ if (nSA > 0 && nSA != nr)
+ {
+ gmx_fatal(FARGS, "Not enough annealing values: %d (for %d groups)\n", nSA, nr);
+ }
+ else
+ {
+ snew(ir->opts.annealing, nr);
+ snew(ir->opts.anneal_npoints, nr);
+ snew(ir->opts.anneal_time, nr);
+ snew(ir->opts.anneal_temp, nr);
+ for (i = 0; i < nr; i++)
+ {
+ ir->opts.annealing[i] = eannNO;
+ ir->opts.anneal_npoints[i] = 0;
+ ir->opts.anneal_time[i] = NULL;
+ ir->opts.anneal_temp[i] = NULL;
+ }
+ if (nSA > 0)
+ {
+ bAnneal = FALSE;
+ for (i = 0; i < nr; i++)
+ {
+ if (ptr1[i][0] == 'n' || ptr1[i][0] == 'N')
+ {
+ ir->opts.annealing[i] = eannNO;
+ }
+ else if (ptr1[i][0] == 's' || ptr1[i][0] == 'S')
+ {
+ ir->opts.annealing[i] = eannSINGLE;
+ bAnneal = TRUE;
+ }
+ else if (ptr1[i][0] == 'p' || ptr1[i][0] == 'P')
+ {
+ ir->opts.annealing[i] = eannPERIODIC;
+ bAnneal = TRUE;
+ }
+ }
+ if (bAnneal)
+ {
+ /* Read the other fields too */
+ nSA_points = str_nelem(is->anneal_npoints, MAXPTR, ptr1);
+ if (nSA_points != nSA)
+ {
+ gmx_fatal(FARGS, "Found %d annealing-npoints values for %d groups\n", nSA_points, nSA);
+ }
+ for (k = 0, i = 0; i < nr; i++)
+ {
+ ir->opts.anneal_npoints[i] = strtol(ptr1[i], NULL, 10);
+ if (ir->opts.anneal_npoints[i] == 1)
+ {
+ gmx_fatal(FARGS, "Please specify at least a start and an end point for annealing\n");
+ }
+ snew(ir->opts.anneal_time[i], ir->opts.anneal_npoints[i]);
+ snew(ir->opts.anneal_temp[i], ir->opts.anneal_npoints[i]);
+ k += ir->opts.anneal_npoints[i];
+ }
+
+ nSA_time = str_nelem(is->anneal_time, MAXPTR, ptr1);
+ if (nSA_time != k)
+ {
+ gmx_fatal(FARGS, "Found %d annealing-time values, wanter %d\n", nSA_time, k);
+ }
+ nSA_temp = str_nelem(is->anneal_temp, MAXPTR, ptr2);
+ if (nSA_temp != k)
+ {
+ gmx_fatal(FARGS, "Found %d annealing-temp values, wanted %d\n", nSA_temp, k);
+ }
+
+ for (i = 0, k = 0; i < nr; i++)
+ {
+
+ for (j = 0; j < ir->opts.anneal_npoints[i]; j++)
+ {
+ ir->opts.anneal_time[i][j] = strtod(ptr1[k], NULL);
+ ir->opts.anneal_temp[i][j] = strtod(ptr2[k], NULL);
+ if (j == 0)
+ {
+ if (ir->opts.anneal_time[i][0] > (ir->init_t+GMX_REAL_EPS))
+ {
+ gmx_fatal(FARGS, "First time point for annealing > init_t.\n");
+ }
+ }
+ else
+ {
+ /* j>0 */
+ if (ir->opts.anneal_time[i][j] < ir->opts.anneal_time[i][j-1])
+ {
+ gmx_fatal(FARGS, "Annealing timepoints out of order: t=%f comes after t=%f\n",
+ ir->opts.anneal_time[i][j], ir->opts.anneal_time[i][j-1]);
+ }
+ }
+ if (ir->opts.anneal_temp[i][j] < 0)
+ {
+ gmx_fatal(FARGS, "Found negative temperature in annealing: %f\n", ir->opts.anneal_temp[i][j]);
+ }
+ k++;
+ }
+ }
+ /* Print out some summary information, to make sure we got it right */
+ for (i = 0, k = 0; i < nr; i++)
+ {
+ if (ir->opts.annealing[i] != eannNO)
+ {
+ j = groups->grps[egcTC].nm_ind[i];
+ fprintf(stderr, "Simulated annealing for group %s: %s, %d timepoints\n",
+ *(groups->grpname[j]), eann_names[ir->opts.annealing[i]],
+ ir->opts.anneal_npoints[i]);
+ fprintf(stderr, "Time (ps) Temperature (K)\n");
+ /* All terms except the last one */
+ for (j = 0; j < (ir->opts.anneal_npoints[i]-1); j++)
+ {
+ fprintf(stderr, "%9.1f %5.1f\n", ir->opts.anneal_time[i][j], ir->opts.anneal_temp[i][j]);
+ }
+
+ /* Finally the last one */
+ j = ir->opts.anneal_npoints[i]-1;
+ if (ir->opts.annealing[i] == eannSINGLE)
+ {
+ fprintf(stderr, "%9.1f- %5.1f\n", ir->opts.anneal_time[i][j], ir->opts.anneal_temp[i][j]);
+ }
+ else
+ {
+ fprintf(stderr, "%9.1f %5.1f\n", ir->opts.anneal_time[i][j], ir->opts.anneal_temp[i][j]);
+ if (fabs(ir->opts.anneal_temp[i][j]-ir->opts.anneal_temp[i][0]) > GMX_REAL_EPS)
+ {
+ warning_note(wi, "There is a temperature jump when your annealing loops back.\n");
+ }
+ }
+ }
+ }
+ }
+ }
+ }
+
+ if (ir->ePull != epullNO)
+ {
+ make_pull_groups(ir->pull, is->pull_grp, grps, gnames);
+
+ make_pull_coords(ir->pull);
+ }
+
+ if (ir->bRot)
+ {
+ make_rotation_groups(ir->rot, is->rot_grp, grps, gnames);
+ }
+
+ if (ir->eSwapCoords != eswapNO)
+ {
+ make_swap_groups(ir->swap, swapgrp, splitgrp0, splitgrp1, solgrp, grps, gnames);
+ }
+
+ /* Make indices for IMD session */
+ if (ir->bIMD)
+ {
+ make_IMD_group(ir->imd, is->imd_grp, grps, gnames);
+ }
+
+ nacc = str_nelem(is->acc, MAXPTR, ptr1);
+ nacg = str_nelem(is->accgrps, MAXPTR, ptr2);
+ if (nacg*DIM != nacc)
+ {
+ gmx_fatal(FARGS, "Invalid Acceleration input: %d groups and %d acc. values",
+ nacg, nacc);
+ }
+ do_numbering(natoms, groups, nacg, ptr2, grps, gnames, egcACC,
+ restnm, egrptpALL_GENREST, bVerbose, wi);
+ nr = groups->grps[egcACC].nr;
+ snew(ir->opts.acc, nr);
+ ir->opts.ngacc = nr;
+
+ for (i = k = 0; (i < nacg); i++)
+ {
+ for (j = 0; (j < DIM); j++, k++)
+ {
+ ir->opts.acc[i][j] = strtod(ptr1[k], NULL);
+ }
+ }
+ for (; (i < nr); i++)
+ {
+ for (j = 0; (j < DIM); j++)
+ {
+ ir->opts.acc[i][j] = 0;
+ }
+ }
+
+ nfrdim = str_nelem(is->frdim, MAXPTR, ptr1);
+ nfreeze = str_nelem(is->freeze, MAXPTR, ptr2);
+ if (nfrdim != DIM*nfreeze)
+ {
+ gmx_fatal(FARGS, "Invalid Freezing input: %d groups and %d freeze values",
+ nfreeze, nfrdim);
+ }
+ do_numbering(natoms, groups, nfreeze, ptr2, grps, gnames, egcFREEZE,
+ restnm, egrptpALL_GENREST, bVerbose, wi);
+ nr = groups->grps[egcFREEZE].nr;
+ ir->opts.ngfrz = nr;
+ snew(ir->opts.nFreeze, nr);
+ for (i = k = 0; (i < nfreeze); i++)
+ {
+ for (j = 0; (j < DIM); j++, k++)
+ {
+ ir->opts.nFreeze[i][j] = (gmx_strncasecmp(ptr1[k], "Y", 1) == 0);
+ if (!ir->opts.nFreeze[i][j])
+ {
+ if (gmx_strncasecmp(ptr1[k], "N", 1) != 0)
+ {
+ sprintf(warnbuf, "Please use Y(ES) or N(O) for freezedim only "
+ "(not %s)", ptr1[k]);
+ warning(wi, warn_buf);
+ }
+ }
+ }
+ }
+ for (; (i < nr); i++)
+ {
+ for (j = 0; (j < DIM); j++)
+ {
+ ir->opts.nFreeze[i][j] = 0;
+ }
+ }
+
+ nenergy = str_nelem(is->energy, MAXPTR, ptr1);
+ do_numbering(natoms, groups, nenergy, ptr1, grps, gnames, egcENER,
+ restnm, egrptpALL_GENREST, bVerbose, wi);
+ add_wall_energrps(groups, ir->nwall, symtab);
+ ir->opts.ngener = groups->grps[egcENER].nr;
+ nvcm = str_nelem(is->vcm, MAXPTR, ptr1);
+ bRest =
+ do_numbering(natoms, groups, nvcm, ptr1, grps, gnames, egcVCM,
+ restnm, nvcm == 0 ? egrptpALL_GENREST : egrptpPART, bVerbose, wi);
+ if (bRest)
+ {
+ warning(wi, "Some atoms are not part of any center of mass motion removal group.\n"
+ "This may lead to artifacts.\n"
+ "In most cases one should use one group for the whole system.");
+ }
+
+ /* Now we have filled the freeze struct, so we can calculate NRDF */
+ calc_nrdf(mtop, ir, gnames);
+
+ if (v && NULL)
+ {
+ real fac, ntot = 0;
+
+ /* Must check per group! */
+ for (i = 0; (i < ir->opts.ngtc); i++)
+ {
+ ntot += ir->opts.nrdf[i];
+ }
+ if (ntot != (DIM*natoms))
+ {
+ fac = sqrt(ntot/(DIM*natoms));
+ if (bVerbose)
+ {
+ fprintf(stderr, "Scaling velocities by a factor of %.3f to account for constraints\n"
+ "and removal of center of mass motion\n", fac);
+ }
+ for (i = 0; (i < natoms); i++)
+ {
+ svmul(fac, v[i], v[i]);
+ }
+ }
+ }
+
+ nuser = str_nelem(is->user1, MAXPTR, ptr1);
+ do_numbering(natoms, groups, nuser, ptr1, grps, gnames, egcUser1,
+ restnm, egrptpALL_GENREST, bVerbose, wi);
+ nuser = str_nelem(is->user2, MAXPTR, ptr1);
+ do_numbering(natoms, groups, nuser, ptr1, grps, gnames, egcUser2,
+ restnm, egrptpALL_GENREST, bVerbose, wi);
+ nuser = str_nelem(is->x_compressed_groups, MAXPTR, ptr1);
+ do_numbering(natoms, groups, nuser, ptr1, grps, gnames, egcCompressedX,
+ restnm, egrptpONE, bVerbose, wi);
+ nofg = str_nelem(is->orirefitgrp, MAXPTR, ptr1);
+ do_numbering(natoms, groups, nofg, ptr1, grps, gnames, egcORFIT,
+ restnm, egrptpALL_GENREST, bVerbose, wi);
+
+ /* QMMM input processing */
+ nQMg = str_nelem(is->QMMM, MAXPTR, ptr1);
+ nQMmethod = str_nelem(is->QMmethod, MAXPTR, ptr2);
+ nQMbasis = str_nelem(is->QMbasis, MAXPTR, ptr3);
+ if ((nQMmethod != nQMg) || (nQMbasis != nQMg))
+ {
+ gmx_fatal(FARGS, "Invalid QMMM input: %d groups %d basissets"
+ " and %d methods\n", nQMg, nQMbasis, nQMmethod);
+ }
+ /* group rest, if any, is always MM! */
+ do_numbering(natoms, groups, nQMg, ptr1, grps, gnames, egcQMMM,
+ restnm, egrptpALL_GENREST, bVerbose, wi);
+ nr = nQMg; /*atoms->grps[egcQMMM].nr;*/
+ ir->opts.ngQM = nQMg;
+ snew(ir->opts.QMmethod, nr);
+ snew(ir->opts.QMbasis, nr);
+ for (i = 0; i < nr; i++)
+ {
+ /* input consists of strings: RHF CASSCF PM3 .. These need to be
+ * converted to the corresponding enum in names.c
+ */
+ ir->opts.QMmethod[i] = search_QMstring(ptr2[i], eQMmethodNR,
+ eQMmethod_names);
+ ir->opts.QMbasis[i] = search_QMstring(ptr3[i], eQMbasisNR,
+ eQMbasis_names);
+
+ }
+ nQMmult = str_nelem(is->QMmult, MAXPTR, ptr1);
+ nQMcharge = str_nelem(is->QMcharge, MAXPTR, ptr2);
+ nbSH = str_nelem(is->bSH, MAXPTR, ptr3);
+ snew(ir->opts.QMmult, nr);
+ snew(ir->opts.QMcharge, nr);
+ snew(ir->opts.bSH, nr);
+
+ for (i = 0; i < nr; i++)
+ {
+ ir->opts.QMmult[i] = strtol(ptr1[i], NULL, 10);
+ ir->opts.QMcharge[i] = strtol(ptr2[i], NULL, 10);
+ ir->opts.bSH[i] = (gmx_strncasecmp(ptr3[i], "Y", 1) == 0);
+ }
+
+ nCASelec = str_nelem(is->CASelectrons, MAXPTR, ptr1);
+ nCASorb = str_nelem(is->CASorbitals, MAXPTR, ptr2);
+ snew(ir->opts.CASelectrons, nr);
+ snew(ir->opts.CASorbitals, nr);
+ for (i = 0; i < nr; i++)
+ {
+ ir->opts.CASelectrons[i] = strtol(ptr1[i], NULL, 10);
+ ir->opts.CASorbitals[i] = strtol(ptr2[i], NULL, 10);
+ }
+ /* special optimization options */
+
+ nbOPT = str_nelem(is->bOPT, MAXPTR, ptr1);
+ nbTS = str_nelem(is->bTS, MAXPTR, ptr2);
+ snew(ir->opts.bOPT, nr);
+ snew(ir->opts.bTS, nr);
+ for (i = 0; i < nr; i++)
+ {
+ ir->opts.bOPT[i] = (gmx_strncasecmp(ptr1[i], "Y", 1) == 0);
+ ir->opts.bTS[i] = (gmx_strncasecmp(ptr2[i], "Y", 1) == 0);
+ }
+ nSAon = str_nelem(is->SAon, MAXPTR, ptr1);
+ nSAoff = str_nelem(is->SAoff, MAXPTR, ptr2);
+ nSAsteps = str_nelem(is->SAsteps, MAXPTR, ptr3);
+ snew(ir->opts.SAon, nr);
+ snew(ir->opts.SAoff, nr);
+ snew(ir->opts.SAsteps, nr);
+
+ for (i = 0; i < nr; i++)
+ {
+ ir->opts.SAon[i] = strtod(ptr1[i], NULL);
+ ir->opts.SAoff[i] = strtod(ptr2[i], NULL);
+ ir->opts.SAsteps[i] = strtol(ptr3[i], NULL, 10);
+ }
+ /* end of QMMM input */
+
+ if (bVerbose)
+ {
+ for (i = 0; (i < egcNR); i++)
+ {
+ fprintf(stderr, "%-16s has %d element(s):", gtypes[i], groups->grps[i].nr);
+ for (j = 0; (j < groups->grps[i].nr); j++)
+ {
+ fprintf(stderr, " %s", *(groups->grpname[groups->grps[i].nm_ind[j]]));
+ }
+ fprintf(stderr, "\n");
+ }
+ }
+
+ nr = groups->grps[egcENER].nr;
+ snew(ir->opts.egp_flags, nr*nr);
+
+ bExcl = do_egp_flag(ir, groups, "energygrp-excl", is->egpexcl, EGP_EXCL);
+ if (bExcl && ir->cutoff_scheme == ecutsVERLET)
+ {
+ warning_error(wi, "Energy group exclusions are not (yet) implemented for the Verlet scheme");
+ }
+ if (bExcl && EEL_FULL(ir->coulombtype))
+ {
+ warning(wi, "Can not exclude the lattice Coulomb energy between energy groups");
+ }
+
+ bTable = do_egp_flag(ir, groups, "energygrp-table", is->egptable, EGP_TABLE);
+ if (bTable && !(ir->vdwtype == evdwUSER) &&
+ !(ir->coulombtype == eelUSER) && !(ir->coulombtype == eelPMEUSER) &&
+ !(ir->coulombtype == eelPMEUSERSWITCH))
+ {
+ gmx_fatal(FARGS, "Can only have energy group pair tables in combination with user tables for VdW and/or Coulomb");
+ }
+
+ decode_cos(is->efield_x, &(ir->ex[XX]));
+ decode_cos(is->efield_xt, &(ir->et[XX]));
+ decode_cos(is->efield_y, &(ir->ex[YY]));
+ decode_cos(is->efield_yt, &(ir->et[YY]));
+ decode_cos(is->efield_z, &(ir->ex[ZZ]));
+ decode_cos(is->efield_zt, &(ir->et[ZZ]));
+
+ if (ir->bAdress)
+ {
+ do_adress_index(ir->adress, groups, gnames, &(ir->opts), wi);
+ }
+
+ for (i = 0; (i < grps->nr); i++)
+ {
+ sfree(gnames[i]);
+ }
+ sfree(gnames);
+ done_blocka(grps);
+ sfree(grps);
+
+}
+
+
+
+static void check_disre(gmx_mtop_t *mtop)
+{
+ gmx_ffparams_t *ffparams;
+ t_functype *functype;
+ t_iparams *ip;
+ int i, ndouble, ftype;
+ int label, old_label;
+
+ if (gmx_mtop_ftype_count(mtop, F_DISRES) > 0)
+ {
+ ffparams = &mtop->ffparams;
+ functype = ffparams->functype;
+ ip = ffparams->iparams;
+ ndouble = 0;
+ old_label = -1;
+ for (i = 0; i < ffparams->ntypes; i++)
+ {
+ ftype = functype[i];
+ if (ftype == F_DISRES)
+ {
+ label = ip[i].disres.label;
+ if (label == old_label)
+ {
+ fprintf(stderr, "Distance restraint index %d occurs twice\n", label);
+ ndouble++;
+ }
+ old_label = label;
+ }
+ }
+ if (ndouble > 0)
+ {
+ gmx_fatal(FARGS, "Found %d double distance restraint indices,\n"
+ "probably the parameters for multiple pairs in one restraint "
+ "are not identical\n", ndouble);
+ }
+ }
+}
+
+static gmx_bool absolute_reference(t_inputrec *ir, gmx_mtop_t *sys,
+ gmx_bool posres_only,
+ ivec AbsRef)
+{
+ int d, g, i;
+ gmx_mtop_ilistloop_t iloop;
+ t_ilist *ilist;
+ int nmol;
+ t_iparams *pr;
+
+ clear_ivec(AbsRef);
+
+ if (!posres_only)
+ {
+ /* Check the COM */
+ for (d = 0; d < DIM; d++)
+ {
+ AbsRef[d] = (d < ndof_com(ir) ? 0 : 1);
+ }
+ /* Check for freeze groups */
+ for (g = 0; g < ir->opts.ngfrz; g++)
+ {
+ for (d = 0; d < DIM; d++)
+ {
+ if (ir->opts.nFreeze[g][d] != 0)
+ {
+ AbsRef[d] = 1;
+ }
+ }
+ }
+ }
+
+ /* Check for position restraints */
+ iloop = gmx_mtop_ilistloop_init(sys);
+ while (gmx_mtop_ilistloop_next(iloop, &ilist, &nmol))
+ {
+ if (nmol > 0 &&
+ (AbsRef[XX] == 0 || AbsRef[YY] == 0 || AbsRef[ZZ] == 0))
+ {
+ for (i = 0; i < ilist[F_POSRES].nr; i += 2)
+ {
+ pr = &sys->ffparams.iparams[ilist[F_POSRES].iatoms[i]];
+ for (d = 0; d < DIM; d++)
+ {
+ if (pr->posres.fcA[d] != 0)
+ {
+ AbsRef[d] = 1;
+ }
+ }
+ }
+ for (i = 0; i < ilist[F_FBPOSRES].nr; i += 2)
+ {
+ /* Check for flat-bottom posres */
+ pr = &sys->ffparams.iparams[ilist[F_FBPOSRES].iatoms[i]];
+ if (pr->fbposres.k != 0)
+ {
+ switch (pr->fbposres.geom)
+ {
+ case efbposresSPHERE:
+ AbsRef[XX] = AbsRef[YY] = AbsRef[ZZ] = 1;
+ break;
+ case efbposresCYLINDER:
+ AbsRef[XX] = AbsRef[YY] = 1;
+ break;
+ case efbposresX: /* d=XX */
+ case efbposresY: /* d=YY */
+ case efbposresZ: /* d=ZZ */
+ d = pr->fbposres.geom - efbposresX;
+ AbsRef[d] = 1;
+ break;
+ default:
+ gmx_fatal(FARGS, " Invalid geometry for flat-bottom position restraint.\n"
+ "Expected nr between 1 and %d. Found %d\n", efbposresNR-1,
+ pr->fbposres.geom);
+ }
+ }
+ }
+ }
+ }
+
+ return (AbsRef[XX] != 0 && AbsRef[YY] != 0 && AbsRef[ZZ] != 0);
+}
+
+static void
+check_combination_rule_differences(const gmx_mtop_t *mtop, int state,
+ gmx_bool *bC6ParametersWorkWithGeometricRules,
+ gmx_bool *bC6ParametersWorkWithLBRules,
+ gmx_bool *bLBRulesPossible)
+{
+ int ntypes, tpi, tpj, thisLBdiff, thisgeomdiff;
+ int *typecount;
+ real tol;
+ double geometricdiff, LBdiff;
+ double c6i, c6j, c12i, c12j;
+ double c6, c6_geometric, c6_LB;
+ double sigmai, sigmaj, epsi, epsj;
+ gmx_bool bCanDoLBRules, bCanDoGeometricRules;
+ const char *ptr;
+
+ /* A tolerance of 1e-5 seems reasonable for (possibly hand-typed)
+ * force-field floating point parameters.
+ */
+ tol = 1e-5;
+ ptr = getenv("GMX_LJCOMB_TOL");
+ if (ptr != NULL)
+ {
+ double dbl;
+
+ sscanf(ptr, "%lf", &dbl);
+ tol = dbl;
+ }
+
+ *bC6ParametersWorkWithLBRules = TRUE;
+ *bC6ParametersWorkWithGeometricRules = TRUE;
+ bCanDoLBRules = TRUE;
+ bCanDoGeometricRules = TRUE;
+ ntypes = mtop->ffparams.atnr;
+ snew(typecount, ntypes);
+ gmx_mtop_count_atomtypes(mtop, state, typecount);
+ geometricdiff = LBdiff = 0.0;
+ *bLBRulesPossible = TRUE;
+ for (tpi = 0; tpi < ntypes; ++tpi)
+ {
+ c6i = mtop->ffparams.iparams[(ntypes + 1) * tpi].lj.c6;
+ c12i = mtop->ffparams.iparams[(ntypes + 1) * tpi].lj.c12;
+ for (tpj = tpi; tpj < ntypes; ++tpj)
+ {
+ c6j = mtop->ffparams.iparams[(ntypes + 1) * tpj].lj.c6;
+ c12j = mtop->ffparams.iparams[(ntypes + 1) * tpj].lj.c12;
+ c6 = mtop->ffparams.iparams[ntypes * tpi + tpj].lj.c6;
+ c6_geometric = sqrt(c6i * c6j);
+ if (!gmx_numzero(c6_geometric))
+ {
+ if (!gmx_numzero(c12i) && !gmx_numzero(c12j))
+ {
+ sigmai = pow(c12i / c6i, 1.0/6.0);
+ sigmaj = pow(c12j / c6j, 1.0/6.0);
+ epsi = c6i * c6i /(4.0 * c12i);
+ epsj = c6j * c6j /(4.0 * c12j);
+ c6_LB = 4.0 * pow(epsi * epsj, 1.0/2.0) * pow(0.5 * (sigmai + sigmaj), 6);
+ }
+ else
+ {
+ *bLBRulesPossible = FALSE;
+ c6_LB = c6_geometric;
+ }
+ bCanDoLBRules = gmx_within_tol(c6_LB, c6, tol);
+ }
+
+ if (FALSE == bCanDoLBRules)
+ {
+ *bC6ParametersWorkWithLBRules = FALSE;
+ }
+
+ bCanDoGeometricRules = gmx_within_tol(c6_geometric, c6, tol);
+
+ if (FALSE == bCanDoGeometricRules)
+ {
+ *bC6ParametersWorkWithGeometricRules = FALSE;
+ }
+ }
+ }
+ sfree(typecount);
+}
+
+static void
+check_combination_rules(const t_inputrec *ir, const gmx_mtop_t *mtop,
+ warninp_t wi)
+{
+ char err_buf[256];
+ gmx_bool bLBRulesPossible, bC6ParametersWorkWithGeometricRules, bC6ParametersWorkWithLBRules;
+
+ check_combination_rule_differences(mtop, 0,
+ &bC6ParametersWorkWithGeometricRules,
+ &bC6ParametersWorkWithLBRules,
+ &bLBRulesPossible);
+ if (ir->ljpme_combination_rule == eljpmeLB)
+ {
+ if (FALSE == bC6ParametersWorkWithLBRules || FALSE == bLBRulesPossible)
+ {
+ warning(wi, "You are using arithmetic-geometric combination rules "
+ "in LJ-PME, but your non-bonded C6 parameters do not "
+ "follow these rules.");
+ }
+ }
+ else
+ {
+ if (FALSE == bC6ParametersWorkWithGeometricRules)
+ {
+ if (ir->eDispCorr != edispcNO)
+ {
+ warning_note(wi, "You are using geometric combination rules in "
+ "LJ-PME, but your non-bonded C6 parameters do "
+ "not follow these rules. "
+ "This will introduce very small errors in the forces and energies in "
+ "your simulations. Dispersion correction will correct total energy "
+ "and/or pressure for isotropic systems, but not forces or surface tensions.");
+ }
+ else
+ {
+ warning_note(wi, "You are using geometric combination rules in "
+ "LJ-PME, but your non-bonded C6 parameters do "
+ "not follow these rules. "
+ "This will introduce very small errors in the forces and energies in "
+ "your simulations. If your system is homogeneous, consider using dispersion correction "
+ "for the total energy and pressure.");
+ }
+ }
+ }
+}
+
+void triple_check(const char *mdparin, t_inputrec *ir, gmx_mtop_t *sys,
+ warninp_t wi)
+{
+ char err_buf[STRLEN];
+ int i, m, c, nmol, npct;
+ gmx_bool bCharge, bAcc;
+ real gdt_max, *mgrp, mt;
+ rvec acc;
+ gmx_mtop_atomloop_block_t aloopb;
+ gmx_mtop_atomloop_all_t aloop;
+ t_atom *atom;
+ ivec AbsRef;
+ char warn_buf[STRLEN];
+
+ set_warning_line(wi, mdparin, -1);
+
+ if (ir->cutoff_scheme == ecutsVERLET &&
+ ir->verletbuf_tol > 0 &&
+ ir->nstlist > 1 &&
+ ((EI_MD(ir->eI) || EI_SD(ir->eI)) &&
+ (ir->etc == etcVRESCALE || ir->etc == etcBERENDSEN)))
+ {
+ /* Check if a too small Verlet buffer might potentially
+ * cause more drift than the thermostat can couple off.
+ */
+ /* Temperature error fraction for warning and suggestion */
+ const real T_error_warn = 0.002;
+ const real T_error_suggest = 0.001;
+ /* For safety: 2 DOF per atom (typical with constraints) */
+ const real nrdf_at = 2;
+ real T, tau, max_T_error;
+ int i;
+
+ T = 0;
+ tau = 0;
+ for (i = 0; i < ir->opts.ngtc; i++)
+ {
+ T = max(T, ir->opts.ref_t[i]);
+ tau = max(tau, ir->opts.tau_t[i]);
+ }
+ if (T > 0)
+ {
+ /* This is a worst case estimate of the temperature error,
+ * assuming perfect buffer estimation and no cancelation
+ * of errors. The factor 0.5 is because energy distributes
+ * equally over Ekin and Epot.
+ */
+ max_T_error = 0.5*tau*ir->verletbuf_tol/(nrdf_at*BOLTZ*T);
+ if (max_T_error > T_error_warn)
+ {
+ sprintf(warn_buf, "With a verlet-buffer-tolerance of %g kJ/mol/ps, a reference temperature of %g and a tau_t of %g, your temperature might be off by up to %.1f%%. To ensure the error is below %.1f%%, decrease verlet-buffer-tolerance to %.0e or decrease tau_t.",
+ ir->verletbuf_tol, T, tau,
+ 100*max_T_error,
+ 100*T_error_suggest,
+ ir->verletbuf_tol*T_error_suggest/max_T_error);
+ warning(wi, warn_buf);
+ }
+ }
+ }
+
+ if (ETC_ANDERSEN(ir->etc))
+ {
+ int i;
+
+ for (i = 0; i < ir->opts.ngtc; i++)
+ {
+ sprintf(err_buf, "all tau_t must currently be equal using Andersen temperature control, violated for group %d", i);
+ CHECK(ir->opts.tau_t[0] != ir->opts.tau_t[i]);
+ sprintf(err_buf, "all tau_t must be postive using Andersen temperature control, tau_t[%d]=%10.6f",
+ i, ir->opts.tau_t[i]);
+ CHECK(ir->opts.tau_t[i] < 0);
+ }
+
+ for (i = 0; i < ir->opts.ngtc; i++)
+ {
+ int nsteps = (int)(ir->opts.tau_t[i]/ir->delta_t);
+ sprintf(err_buf, "tau_t/delta_t for group %d for temperature control method %s must be a multiple of nstcomm (%d), as velocities of atoms in coupled groups are randomized every time step. The input tau_t (%8.3f) leads to %d steps per randomization", i, etcoupl_names[ir->etc], ir->nstcomm, ir->opts.tau_t[i], nsteps);
+ CHECK((nsteps % ir->nstcomm) && (ir->etc == etcANDERSENMASSIVE));
+ }
+ }
+
+ if (EI_DYNAMICS(ir->eI) && !EI_SD(ir->eI) && ir->eI != eiBD &&
+ ir->comm_mode == ecmNO &&
+ !(absolute_reference(ir, sys, FALSE, AbsRef) || ir->nsteps <= 10) &&
+ !ETC_ANDERSEN(ir->etc))
+ {
+ warning(wi, "You are not using center of mass motion removal (mdp option comm-mode), numerical rounding errors can lead to build up of kinetic energy of the center of mass");
+ }
+
+ /* Check for pressure coupling with absolute position restraints */
+ if (ir->epc != epcNO && ir->refcoord_scaling == erscNO)
+ {
+ absolute_reference(ir, sys, TRUE, AbsRef);
+ {
+ for (m = 0; m < DIM; m++)
+ {
+ if (AbsRef[m] && norm2(ir->compress[m]) > 0)
+ {
+ warning(wi, "You are using pressure coupling with absolute position restraints, this will give artifacts. Use the refcoord_scaling option.");
+ break;
+ }
+ }
+ }
+ }
+
+ bCharge = FALSE;
+ aloopb = gmx_mtop_atomloop_block_init(sys);
+ while (gmx_mtop_atomloop_block_next(aloopb, &atom, &nmol))
+ {
+ if (atom->q != 0 || atom->qB != 0)
+ {
+ bCharge = TRUE;
+ }
+ }
+
+ if (!bCharge)
+ {
+ if (EEL_FULL(ir->coulombtype))
+ {
+ sprintf(err_buf,
+ "You are using full electrostatics treatment %s for a system without charges.\n"
+ "This costs a lot of performance for just processing zeros, consider using %s instead.\n",
+ EELTYPE(ir->coulombtype), EELTYPE(eelCUT));
+ warning(wi, err_buf);
+ }
+ }
+ else
+ {
+ if (ir->coulombtype == eelCUT && ir->rcoulomb > 0 && !ir->implicit_solvent)
+ {
+ sprintf(err_buf,
+ "You are using a plain Coulomb cut-off, which might produce artifacts.\n"
+ "You might want to consider using %s electrostatics.\n",
+ EELTYPE(eelPME));
+ warning_note(wi, err_buf);
+ }
+ }
+
+ /* Check if combination rules used in LJ-PME are the same as in the force field */
+ if (EVDW_PME(ir->vdwtype))
+ {
+ check_combination_rules(ir, sys, wi);
+ }
+
+ /* Generalized reaction field */
+ if (ir->opts.ngtc == 0)
+ {
+ sprintf(err_buf, "No temperature coupling while using coulombtype %s",
+ eel_names[eelGRF]);
+ CHECK(ir->coulombtype == eelGRF);
+ }
+ else
+ {
+ sprintf(err_buf, "When using coulombtype = %s"
+ " ref-t for temperature coupling should be > 0",
+ eel_names[eelGRF]);
+ CHECK((ir->coulombtype == eelGRF) && (ir->opts.ref_t[0] <= 0));
+ }
+
+ if (ir->eI == eiSD1 &&
+ (gmx_mtop_ftype_count(sys, F_CONSTR) > 0 ||
+ gmx_mtop_ftype_count(sys, F_SETTLE) > 0))
+ {
+ sprintf(warn_buf, "With constraints integrator %s is less accurate, consider using %s instead", ei_names[ir->eI], ei_names[eiSD2]);
+ warning_note(wi, warn_buf);
+ }
+
+ bAcc = FALSE;
+ for (i = 0; (i < sys->groups.grps[egcACC].nr); i++)
+ {
+ for (m = 0; (m < DIM); m++)
+ {
+ if (fabs(ir->opts.acc[i][m]) > 1e-6)
+ {
+ bAcc = TRUE;
+ }
+ }
+ }
+ if (bAcc)
+ {
+ clear_rvec(acc);
+ snew(mgrp, sys->groups.grps[egcACC].nr);
+ aloop = gmx_mtop_atomloop_all_init(sys);
+ while (gmx_mtop_atomloop_all_next(aloop, &i, &atom))
+ {
+ mgrp[ggrpnr(&sys->groups, egcACC, i)] += atom->m;
+ }
+ mt = 0.0;
+ for (i = 0; (i < sys->groups.grps[egcACC].nr); i++)
+ {
+ for (m = 0; (m < DIM); m++)
+ {
+ acc[m] += ir->opts.acc[i][m]*mgrp[i];
+ }
+ mt += mgrp[i];
+ }
+ for (m = 0; (m < DIM); m++)
+ {
+ if (fabs(acc[m]) > 1e-6)
+ {
+ const char *dim[DIM] = { "X", "Y", "Z" };
+ fprintf(stderr,
+ "Net Acceleration in %s direction, will %s be corrected\n",
+ dim[m], ir->nstcomm != 0 ? "" : "not");
+ if (ir->nstcomm != 0 && m < ndof_com(ir))
+ {
+ acc[m] /= mt;
+ for (i = 0; (i < sys->groups.grps[egcACC].nr); i++)
+ {
+ ir->opts.acc[i][m] -= acc[m];
+ }
+ }
+ }
+ }
+ sfree(mgrp);
+ }
+
+ if (ir->efep != efepNO && ir->fepvals->sc_alpha != 0 &&
+ !gmx_within_tol(sys->ffparams.reppow, 12.0, 10*GMX_DOUBLE_EPS))
+ {
+ gmx_fatal(FARGS, "Soft-core interactions are only supported with VdW repulsion power 12");
+ }
+
+ if (ir->ePull != epullNO)
+ {
+ gmx_bool bPullAbsoluteRef;
+
+ bPullAbsoluteRef = FALSE;
+ for (i = 0; i < ir->pull->ncoord; i++)
+ {
+ bPullAbsoluteRef = bPullAbsoluteRef ||
+ ir->pull->coord[i].group[0] == 0 ||
+ ir->pull->coord[i].group[1] == 0;
+ }
+ if (bPullAbsoluteRef)
+ {
+ absolute_reference(ir, sys, FALSE, AbsRef);
+ for (m = 0; m < DIM; m++)
+ {
+ if (ir->pull->dim[m] && !AbsRef[m])
+ {
+ warning(wi, "You are using an absolute reference for pulling, but the rest of the system does not have an absolute reference. This will lead to artifacts.");
+ break;
+ }
+ }
+ }
+
+ if (ir->pull->eGeom == epullgDIRPBC)
+ {
+ for (i = 0; i < 3; i++)
+ {
+ for (m = 0; m <= i; m++)
+ {
+ if ((ir->epc != epcNO && ir->compress[i][m] != 0) ||
+ ir->deform[i][m] != 0)
+ {
+ for (c = 0; c < ir->pull->ncoord; c++)
+ {
+ if (ir->pull->coord[c].vec[m] != 0)
+ {
+ gmx_fatal(FARGS, "Can not have dynamic box while using pull geometry '%s' (dim %c)", EPULLGEOM(ir->pull->eGeom), 'x'+m);
+ }
+ }
+ }
+ }
+ }
+ }
+ }
+
+ check_disre(sys);
+}
+
+void double_check(t_inputrec *ir, matrix box, gmx_bool bConstr, warninp_t wi)
+{
+ real min_size;
+ gmx_bool bTWIN;
+ char warn_buf[STRLEN];
+ const char *ptr;
+
+ ptr = check_box(ir->ePBC, box);
+ if (ptr)
+ {
+ warning_error(wi, ptr);
+ }
+
+ if (bConstr && ir->eConstrAlg == econtSHAKE)
+ {
+ if (ir->shake_tol <= 0.0)
+ {
+ sprintf(warn_buf, "ERROR: shake-tol must be > 0 instead of %g\n",
+ ir->shake_tol);
+ warning_error(wi, warn_buf);
+ }
+
+ if (IR_TWINRANGE(*ir) && ir->nstlist > 1)
+ {
+ sprintf(warn_buf, "With twin-range cut-off's and SHAKE the virial and the pressure are incorrect.");
+ if (ir->epc == epcNO)
+ {
+ warning(wi, warn_buf);
+ }
+ else
+ {
+ warning_error(wi, warn_buf);
+ }
+ }
+ }
+
+ if ( (ir->eConstrAlg == econtLINCS) && bConstr)
+ {
+ /* If we have Lincs constraints: */
+ if (ir->eI == eiMD && ir->etc == etcNO &&
+ ir->eConstrAlg == econtLINCS && ir->nLincsIter == 1)
+ {
+ sprintf(warn_buf, "For energy conservation with LINCS, lincs_iter should be 2 or larger.\n");
+ warning_note(wi, warn_buf);
+ }
+
+ if ((ir->eI == eiCG || ir->eI == eiLBFGS) && (ir->nProjOrder < 8))
+ {
+ sprintf(warn_buf, "For accurate %s with LINCS constraints, lincs-order should be 8 or more.", ei_names[ir->eI]);
+ warning_note(wi, warn_buf);
+ }
+ if (ir->epc == epcMTTK)
+ {
+ warning_error(wi, "MTTK not compatible with lincs -- use shake instead.");
+ }
+ }
+
+ if (bConstr && ir->epc == epcMTTK)
+ {
+ warning_note(wi, "MTTK with constraints is deprecated, and will be removed in GROMACS 5.1");
+ }
+
+ if (ir->LincsWarnAngle > 90.0)
+ {
+ sprintf(warn_buf, "lincs-warnangle can not be larger than 90 degrees, setting it to 90.\n");
+ warning(wi, warn_buf);
+ ir->LincsWarnAngle = 90.0;
+ }
+
+ if (ir->ePBC != epbcNONE)
+ {
+ if (ir->nstlist == 0)
+ {
+ warning(wi, "With nstlist=0 atoms are only put into the box at step 0, therefore drifting atoms might cause the simulation to crash.");
+ }
+ bTWIN = (ir->rlistlong > ir->rlist);
+ if (ir->ns_type == ensGRID)
+ {
+ if (sqr(ir->rlistlong) >= max_cutoff2(ir->ePBC, box))
+ {
+ sprintf(warn_buf, "ERROR: The cut-off length is longer than half the shortest box vector or longer than the smallest box diagonal element. Increase the box size or decrease %s.\n",
+ bTWIN ? (ir->rcoulomb == ir->rlistlong ? "rcoulomb" : "rvdw") : "rlist");
+ warning_error(wi, warn_buf);
+ }
+ }
+ else
+ {
+ min_size = min(box[XX][XX], min(box[YY][YY], box[ZZ][ZZ]));
+ if (2*ir->rlistlong >= min_size)
+ {
+ sprintf(warn_buf, "ERROR: One of the box lengths is smaller than twice the cut-off length. Increase the box size or decrease rlist.");
+ warning_error(wi, warn_buf);
+ if (TRICLINIC(box))
+ {
+ fprintf(stderr, "Grid search might allow larger cut-off's than simple search with triclinic boxes.");
+ }
+ }
+ }
+ }
+}
+
+void check_chargegroup_radii(const gmx_mtop_t *mtop, const t_inputrec *ir,
+ rvec *x,
+ warninp_t wi)
+{
+ real rvdw1, rvdw2, rcoul1, rcoul2;
+ char warn_buf[STRLEN];
+
+ calc_chargegroup_radii(mtop, x, &rvdw1, &rvdw2, &rcoul1, &rcoul2);
+
+ if (rvdw1 > 0)
+ {
+ printf("Largest charge group radii for Van der Waals: %5.3f, %5.3f nm\n",
+ rvdw1, rvdw2);
+ }
+ if (rcoul1 > 0)
+ {
+ printf("Largest charge group radii for Coulomb: %5.3f, %5.3f nm\n",
+ rcoul1, rcoul2);
+ }
+
+ if (ir->rlist > 0)
+ {
+ if (rvdw1 + rvdw2 > ir->rlist ||
+ rcoul1 + rcoul2 > ir->rlist)
+ {
+ sprintf(warn_buf,
+ "The sum of the two largest charge group radii (%f) "
+ "is larger than rlist (%f)\n",
+ max(rvdw1+rvdw2, rcoul1+rcoul2), ir->rlist);
+ warning(wi, warn_buf);
+ }
+ else
+ {
+ /* Here we do not use the zero at cut-off macro,
+ * since user defined interactions might purposely
+ * not be zero at the cut-off.
+ */
+ if (ir_vdw_is_zero_at_cutoff(ir) &&
+ rvdw1 + rvdw2 > ir->rlistlong - ir->rvdw)
+ {
+ sprintf(warn_buf, "The sum of the two largest charge group "
+ "radii (%f) is larger than %s (%f) - rvdw (%f).\n"
+ "With exact cut-offs, better performance can be "
+ "obtained with cutoff-scheme = %s, because it "
+ "does not use charge groups at all.",
+ rvdw1+rvdw2,
+ ir->rlistlong > ir->rlist ? "rlistlong" : "rlist",
+ ir->rlistlong, ir->rvdw,
+ ecutscheme_names[ecutsVERLET]);
+ if (ir_NVE(ir))
+ {
+ warning(wi, warn_buf);
+ }
+ else
+ {
+ warning_note(wi, warn_buf);
+ }
+ }
+ if (ir_coulomb_is_zero_at_cutoff(ir) &&
+ rcoul1 + rcoul2 > ir->rlistlong - ir->rcoulomb)
+ {
+ sprintf(warn_buf, "The sum of the two largest charge group radii (%f) is larger than %s (%f) - rcoulomb (%f).\n"
+ "With exact cut-offs, better performance can be obtained with cutoff-scheme = %s, because it does not use charge groups at all.",
+ rcoul1+rcoul2,
+ ir->rlistlong > ir->rlist ? "rlistlong" : "rlist",
+ ir->rlistlong, ir->rcoulomb,
+ ecutscheme_names[ecutsVERLET]);
+ if (ir_NVE(ir))
+ {
+ warning(wi, warn_buf);
+ }
+ else
+ {
+ warning_note(wi, warn_buf);
+ }
+ }
+ }
+ }
+}
--- /dev/null
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
+ * Copyright (c) 2001-2004, The GROMACS development team.
+ * Copyright (c) 2013,2014, by the GROMACS development team, led by
+ * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+ * and including many others, as listed in the AUTHORS file in the
+ * top-level source directory and at http://www.gromacs.org.
+ *
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
+ * of the License, or (at your option) any later version.
+ *
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+ *
+ * If you want to redistribute modifications to GROMACS, please
+ * consider that scientific software is very special. Version
+ * control is crucial - bugs must be traceable. We will be happy to
+ * consider code for inclusion in the official distribution, but
+ * derived work must not be called official GROMACS. Details are found
+ * in the README & COPYING files - if they are missing, get the
+ * official version at http://www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the research papers on the package. Check out http://www.gromacs.org.
+ */
+#ifdef HAVE_CONFIG_H
+#include <config.h>
+#endif
+
+#include <math.h>
+#include <string.h>
+#include <assert.h>
+#include "sysstuff.h"
+#include "typedefs.h"
+#include "types/commrec.h"
+#include "vec.h"
+#include "gromacs/math/utilities.h"
+#include "macros.h"
+#include "gromacs/utility/smalloc.h"
+#include "macros.h"
+#include "gmx_fatal.h"
+#include "physics.h"
+#include "force.h"
+#include "tables.h"
+#include "nonbonded.h"
+#include "invblock.h"
+#include "names.h"
+#include "network.h"
+#include "pbc.h"
+#include "ns.h"
+#include "mshift.h"
+#include "txtdump.h"
+#include "coulomb.h"
+#include "md_support.h"
+#include "md_logging.h"
+#include "domdec.h"
+#include "qmmm.h"
+#include "copyrite.h"
+#include "mtop_util.h"
+#include "nbnxn_simd.h"
+#include "nbnxn_search.h"
+#include "nbnxn_atomdata.h"
+#include "nbnxn_consts.h"
+#include "gmx_omp_nthreads.h"
+#include "gmx_detect_hardware.h"
+#include "inputrec.h"
+
+#include "types/nbnxn_cuda_types_ext.h"
+#include "gpu_utils.h"
+#include "nbnxn_cuda_data_mgmt.h"
+#include "pmalloc_cuda.h"
+
+t_forcerec *mk_forcerec(void)
+{
+ t_forcerec *fr;
+
+ snew(fr, 1);
+
+ return fr;
+}
+
+#ifdef DEBUG
+static void pr_nbfp(FILE *fp, real *nbfp, gmx_bool bBHAM, int atnr)
+{
+ int i, j;
+
+ for (i = 0; (i < atnr); i++)
+ {
+ for (j = 0; (j < atnr); j++)
+ {
+ fprintf(fp, "%2d - %2d", i, j);
+ if (bBHAM)
+ {
+ fprintf(fp, " a=%10g, b=%10g, c=%10g\n", BHAMA(nbfp, atnr, i, j),
+ BHAMB(nbfp, atnr, i, j), BHAMC(nbfp, atnr, i, j)/6.0);
+ }
+ else
+ {
+ fprintf(fp, " c6=%10g, c12=%10g\n", C6(nbfp, atnr, i, j)/6.0,
+ C12(nbfp, atnr, i, j)/12.0);
+ }
+ }
+ }
+}
+#endif
+
+static real *mk_nbfp(const gmx_ffparams_t *idef, gmx_bool bBHAM)
+{
+ real *nbfp;
+ int i, j, k, atnr;
+
+ atnr = idef->atnr;
+ if (bBHAM)
+ {
+ snew(nbfp, 3*atnr*atnr);
+ for (i = k = 0; (i < atnr); i++)
+ {
+ for (j = 0; (j < atnr); j++, k++)
+ {
+ BHAMA(nbfp, atnr, i, j) = idef->iparams[k].bham.a;
+ BHAMB(nbfp, atnr, i, j) = idef->iparams[k].bham.b;
+ /* nbfp now includes the 6.0 derivative prefactor */
+ BHAMC(nbfp, atnr, i, j) = idef->iparams[k].bham.c*6.0;
+ }
+ }
+ }
+ else
+ {
+ snew(nbfp, 2*atnr*atnr);
+ for (i = k = 0; (i < atnr); i++)
+ {
+ for (j = 0; (j < atnr); j++, k++)
+ {
+ /* nbfp now includes the 6.0/12.0 derivative prefactors */
+ C6(nbfp, atnr, i, j) = idef->iparams[k].lj.c6*6.0;
+ C12(nbfp, atnr, i, j) = idef->iparams[k].lj.c12*12.0;
+ }
+ }
+ }
+
+ return nbfp;
+}
+
+static real *make_ljpme_c6grid(const gmx_ffparams_t *idef, t_forcerec *fr)
+{
+ int i, j, k, atnr;
+ real c6, c6i, c6j, c12i, c12j, epsi, epsj, sigmai, sigmaj;
+ real *grid;
+
+ /* For LJ-PME simulations, we correct the energies with the reciprocal space
+ * inside of the cut-off. To do this the non-bonded kernels needs to have
+ * access to the C6-values used on the reciprocal grid in pme.c
+ */
+
+ atnr = idef->atnr;
+ snew(grid, 2*atnr*atnr);
+ for (i = k = 0; (i < atnr); i++)
+ {
+ for (j = 0; (j < atnr); j++, k++)
+ {
+ c6i = idef->iparams[i*(atnr+1)].lj.c6;
+ c12i = idef->iparams[i*(atnr+1)].lj.c12;
+ c6j = idef->iparams[j*(atnr+1)].lj.c6;
+ c12j = idef->iparams[j*(atnr+1)].lj.c12;
+ c6 = sqrt(c6i * c6j);
+ if (fr->ljpme_combination_rule == eljpmeLB
+ && !gmx_numzero(c6) && !gmx_numzero(c12i) && !gmx_numzero(c12j))
+ {
+ sigmai = pow(c12i / c6i, 1.0/6.0);
+ sigmaj = pow(c12j / c6j, 1.0/6.0);
+ epsi = c6i * c6i / c12i;
+ epsj = c6j * c6j / c12j;
+ c6 = sqrt(epsi * epsj) * pow(0.5*(sigmai+sigmaj), 6);
+ }
+ /* Store the elements at the same relative positions as C6 in nbfp in order
+ * to simplify access in the kernels
+ */
+ grid[2*(atnr*i+j)] = c6*6.0;
+ }
+ }
+ return grid;
+}
+
+static real *mk_nbfp_combination_rule(const gmx_ffparams_t *idef, int comb_rule)
+{
+ real *nbfp;
+ int i, j, k, atnr;
+ real c6i, c6j, c12i, c12j, epsi, epsj, sigmai, sigmaj;
+ real c6, c12;
+
+ atnr = idef->atnr;
+ snew(nbfp, 2*atnr*atnr);
+ for (i = 0; i < atnr; ++i)
+ {
+ for (j = 0; j < atnr; ++j)
+ {
+ c6i = idef->iparams[i*(atnr+1)].lj.c6;
+ c12i = idef->iparams[i*(atnr+1)].lj.c12;
+ c6j = idef->iparams[j*(atnr+1)].lj.c6;
+ c12j = idef->iparams[j*(atnr+1)].lj.c12;
+ c6 = sqrt(c6i * c6j);
+ c12 = sqrt(c12i * c12j);
+ if (comb_rule == eCOMB_ARITHMETIC
+ && !gmx_numzero(c6) && !gmx_numzero(c12))
+ {
+ sigmai = pow(c12i / c6i, 1.0/6.0);
+ sigmaj = pow(c12j / c6j, 1.0/6.0);
+ epsi = c6i * c6i / c12i;
+ epsj = c6j * c6j / c12j;
+ c6 = epsi * epsj * pow(0.5*(sigmai+sigmaj), 6);
+ c12 = epsi * epsj * pow(0.5*(sigmai+sigmaj), 12);
+ }
+ C6(nbfp, atnr, i, j) = c6*6.0;
+ C12(nbfp, atnr, i, j) = c12*12.0;
+ }
+ }
+ return nbfp;
+}
+
+/* This routine sets fr->solvent_opt to the most common solvent in the
+ * system, e.g. esolSPC or esolTIP4P. It will also mark each charge group in
+ * the fr->solvent_type array with the correct type (or esolNO).
+ *
+ * Charge groups that fulfill the conditions but are not identical to the
+ * most common one will be marked as esolNO in the solvent_type array.
+ *
+ * TIP3p is identical to SPC for these purposes, so we call it
+ * SPC in the arrays (Apologies to Bill Jorgensen ;-)
+ *
+ * NOTE: QM particle should not
+ * become an optimized solvent. Not even if there is only one charge
+ * group in the Qm
+ */
+
+typedef struct
+{
+ int model;
+ int count;
+ int vdwtype[4];
+ real charge[4];
+} solvent_parameters_t;
+
+static void
+check_solvent_cg(const gmx_moltype_t *molt,
+ int cg0,
+ int nmol,
+ const unsigned char *qm_grpnr,
+ const t_grps *qm_grps,
+ t_forcerec * fr,
+ int *n_solvent_parameters,
+ solvent_parameters_t **solvent_parameters_p,
+ int cginfo,
+ int *cg_sp)
+{
+ const t_blocka *excl;
+ t_atom *atom;
+ int j, k;
+ int j0, j1, nj;
+ gmx_bool perturbed;
+ gmx_bool has_vdw[4];
+ gmx_bool match;
+ real tmp_charge[4] = { 0.0 }; /* init to zero to make gcc4.8 happy */
+ int tmp_vdwtype[4] = { 0 }; /* init to zero to make gcc4.8 happy */
+ int tjA;
+ gmx_bool qm;
+ solvent_parameters_t *solvent_parameters;
+
+ /* We use a list with parameters for each solvent type.
+ * Every time we discover a new molecule that fulfills the basic
+ * conditions for a solvent we compare with the previous entries
+ * in these lists. If the parameters are the same we just increment
+ * the counter for that type, and otherwise we create a new type
+ * based on the current molecule.
+ *
+ * Once we've finished going through all molecules we check which
+ * solvent is most common, and mark all those molecules while we
+ * clear the flag on all others.
+ */
+
+ solvent_parameters = *solvent_parameters_p;
+
+ /* Mark the cg first as non optimized */
+ *cg_sp = -1;
+
+ /* Check if this cg has no exclusions with atoms in other charge groups
+ * and all atoms inside the charge group excluded.
+ * We only have 3 or 4 atom solvent loops.
+ */
+ if (GET_CGINFO_EXCL_INTER(cginfo) ||
+ !GET_CGINFO_EXCL_INTRA(cginfo))
+ {
+ return;
+ }
+
+ /* Get the indices of the first atom in this charge group */
+ j0 = molt->cgs.index[cg0];
+ j1 = molt->cgs.index[cg0+1];
+
+ /* Number of atoms in our molecule */
+ nj = j1 - j0;
+
+ if (debug)
+ {
+ fprintf(debug,
+ "Moltype '%s': there are %d atoms in this charge group\n",
+ *molt->name, nj);
+ }
+
+ /* Check if it could be an SPC (3 atoms) or TIP4p (4) water,
+ * otherwise skip it.
+ */
+ if (nj < 3 || nj > 4)
+ {
+ return;
+ }
+
+ /* Check if we are doing QM on this group */
+ qm = FALSE;
+ if (qm_grpnr != NULL)
+ {
+ for (j = j0; j < j1 && !qm; j++)
+ {
+ qm = (qm_grpnr[j] < qm_grps->nr - 1);
+ }
+ }
+ /* Cannot use solvent optimization with QM */
+ if (qm)
+ {
+ return;
+ }
+
+ atom = molt->atoms.atom;
+
+ /* Still looks like a solvent, time to check parameters */
+
+ /* If it is perturbed (free energy) we can't use the solvent loops,
+ * so then we just skip to the next molecule.
+ */
+ perturbed = FALSE;
+
+ for (j = j0; j < j1 && !perturbed; j++)
+ {
+ perturbed = PERTURBED(atom[j]);
+ }
+
+ if (perturbed)
+ {
+ return;
+ }
+
+ /* Now it's only a question if the VdW and charge parameters
+ * are OK. Before doing the check we compare and see if they are
+ * identical to a possible previous solvent type.
+ * First we assign the current types and charges.
+ */
+ for (j = 0; j < nj; j++)
+ {
+ tmp_vdwtype[j] = atom[j0+j].type;
+ tmp_charge[j] = atom[j0+j].q;
+ }
+
+ /* Does it match any previous solvent type? */
+ for (k = 0; k < *n_solvent_parameters; k++)
+ {
+ match = TRUE;
+
+
+ /* We can only match SPC with 3 atoms and TIP4p with 4 atoms */
+ if ( (solvent_parameters[k].model == esolSPC && nj != 3) ||
+ (solvent_parameters[k].model == esolTIP4P && nj != 4) )
+ {
+ match = FALSE;
+ }
+
+ /* Check that types & charges match for all atoms in molecule */
+ for (j = 0; j < nj && match == TRUE; j++)
+ {
+ if (tmp_vdwtype[j] != solvent_parameters[k].vdwtype[j])
+ {
+ match = FALSE;
+ }
+ if (tmp_charge[j] != solvent_parameters[k].charge[j])
+ {
+ match = FALSE;
+ }
+ }
+ if (match == TRUE)
+ {
+ /* Congratulations! We have a matched solvent.
+ * Flag it with this type for later processing.
+ */
+ *cg_sp = k;
+ solvent_parameters[k].count += nmol;
+
+ /* We are done with this charge group */
+ return;
+ }
+ }
+
+ /* If we get here, we have a tentative new solvent type.
+ * Before we add it we must check that it fulfills the requirements
+ * of the solvent optimized loops. First determine which atoms have
+ * VdW interactions.
+ */
+ for (j = 0; j < nj; j++)
+ {
+ has_vdw[j] = FALSE;
+ tjA = tmp_vdwtype[j];
+
+ /* Go through all other tpes and see if any have non-zero
+ * VdW parameters when combined with this one.
+ */
+ for (k = 0; k < fr->ntype && (has_vdw[j] == FALSE); k++)
+ {
+ /* We already checked that the atoms weren't perturbed,
+ * so we only need to check state A now.
+ */
+ if (fr->bBHAM)
+ {
+ has_vdw[j] = (has_vdw[j] ||
+ (BHAMA(fr->nbfp, fr->ntype, tjA, k) != 0.0) ||
+ (BHAMB(fr->nbfp, fr->ntype, tjA, k) != 0.0) ||
+ (BHAMC(fr->nbfp, fr->ntype, tjA, k) != 0.0));
+ }
+ else
+ {
+ /* Standard LJ */
+ has_vdw[j] = (has_vdw[j] ||
+ (C6(fr->nbfp, fr->ntype, tjA, k) != 0.0) ||
+ (C12(fr->nbfp, fr->ntype, tjA, k) != 0.0));
+ }
+ }
+ }
+
+ /* Now we know all we need to make the final check and assignment. */
+ if (nj == 3)
+ {
+ /* So, is it an SPC?
+ * For this we require thatn all atoms have charge,
+ * the charges on atom 2 & 3 should be the same, and only
+ * atom 1 might have VdW.
+ */
+ if (has_vdw[1] == FALSE &&
+ has_vdw[2] == FALSE &&
+ tmp_charge[0] != 0 &&
+ tmp_charge[1] != 0 &&
+ tmp_charge[2] == tmp_charge[1])
+ {
+ srenew(solvent_parameters, *n_solvent_parameters+1);
+ solvent_parameters[*n_solvent_parameters].model = esolSPC;
+ solvent_parameters[*n_solvent_parameters].count = nmol;
+ for (k = 0; k < 3; k++)
+ {
+ solvent_parameters[*n_solvent_parameters].vdwtype[k] = tmp_vdwtype[k];
+ solvent_parameters[*n_solvent_parameters].charge[k] = tmp_charge[k];
+ }
+
+ *cg_sp = *n_solvent_parameters;
+ (*n_solvent_parameters)++;
+ }
+ }
+ else if (nj == 4)
+ {
+ /* Or could it be a TIP4P?
+ * For this we require thatn atoms 2,3,4 have charge, but not atom 1.
+ * Only atom 1 mght have VdW.
+ */
+ if (has_vdw[1] == FALSE &&
+ has_vdw[2] == FALSE &&
+ has_vdw[3] == FALSE &&
+ tmp_charge[0] == 0 &&
+ tmp_charge[1] != 0 &&
+ tmp_charge[2] == tmp_charge[1] &&
+ tmp_charge[3] != 0)
+ {
+ srenew(solvent_parameters, *n_solvent_parameters+1);
+ solvent_parameters[*n_solvent_parameters].model = esolTIP4P;
+ solvent_parameters[*n_solvent_parameters].count = nmol;
+ for (k = 0; k < 4; k++)
+ {
+ solvent_parameters[*n_solvent_parameters].vdwtype[k] = tmp_vdwtype[k];
+ solvent_parameters[*n_solvent_parameters].charge[k] = tmp_charge[k];
+ }
+
+ *cg_sp = *n_solvent_parameters;
+ (*n_solvent_parameters)++;
+ }
+ }
+
+ *solvent_parameters_p = solvent_parameters;
+}
+
+static void
+check_solvent(FILE * fp,
+ const gmx_mtop_t * mtop,
+ t_forcerec * fr,
+ cginfo_mb_t *cginfo_mb)
+{
+ const t_block * cgs;
+ const t_block * mols;
+ const gmx_moltype_t *molt;
+ int mb, mol, cg_mol, at_offset, cg_offset, am, cgm, i, nmol_ch, nmol;
+ int n_solvent_parameters;
+ solvent_parameters_t *solvent_parameters;
+ int **cg_sp;
+ int bestsp, bestsol;
+
+ if (debug)
+ {
+ fprintf(debug, "Going to determine what solvent types we have.\n");
+ }
+
+ mols = &mtop->mols;
+
+ n_solvent_parameters = 0;
+ solvent_parameters = NULL;
+ /* Allocate temporary array for solvent type */
+ snew(cg_sp, mtop->nmolblock);
+
+ cg_offset = 0;
+ at_offset = 0;
+ for (mb = 0; mb < mtop->nmolblock; mb++)
+ {
+ molt = &mtop->moltype[mtop->molblock[mb].type];
+ cgs = &molt->cgs;
+ /* Here we have to loop over all individual molecules
+ * because we need to check for QMMM particles.
+ */
+ snew(cg_sp[mb], cginfo_mb[mb].cg_mod);
+ nmol_ch = cginfo_mb[mb].cg_mod/cgs->nr;
+ nmol = mtop->molblock[mb].nmol/nmol_ch;
+ for (mol = 0; mol < nmol_ch; mol++)
+ {
+ cgm = mol*cgs->nr;
+ am = mol*cgs->index[cgs->nr];
+ for (cg_mol = 0; cg_mol < cgs->nr; cg_mol++)
+ {
+ check_solvent_cg(molt, cg_mol, nmol,
+ mtop->groups.grpnr[egcQMMM] ?
+ mtop->groups.grpnr[egcQMMM]+at_offset+am : 0,
+ &mtop->groups.grps[egcQMMM],
+ fr,
+ &n_solvent_parameters, &solvent_parameters,
+ cginfo_mb[mb].cginfo[cgm+cg_mol],
+ &cg_sp[mb][cgm+cg_mol]);
+ }
+ }
+ cg_offset += cgs->nr;
+ at_offset += cgs->index[cgs->nr];
+ }
+
+ /* Puh! We finished going through all charge groups.
+ * Now find the most common solvent model.
+ */
+
+ /* Most common solvent this far */
+ bestsp = -2;
+ for (i = 0; i < n_solvent_parameters; i++)
+ {
+ if (bestsp == -2 ||
+ solvent_parameters[i].count > solvent_parameters[bestsp].count)
+ {
+ bestsp = i;
+ }
+ }
+
+ if (bestsp >= 0)
+ {
+ bestsol = solvent_parameters[bestsp].model;
+ }
+ else
+ {
+ bestsol = esolNO;
+ }
+
+#ifdef DISABLE_WATER_NLIST
+ bestsol = esolNO;
+#endif
+
+ fr->nWatMol = 0;
+ for (mb = 0; mb < mtop->nmolblock; mb++)
+ {
+ cgs = &mtop->moltype[mtop->molblock[mb].type].cgs;
+ nmol = (mtop->molblock[mb].nmol*cgs->nr)/cginfo_mb[mb].cg_mod;
+ for (i = 0; i < cginfo_mb[mb].cg_mod; i++)
+ {
+ if (cg_sp[mb][i] == bestsp)
+ {
+ SET_CGINFO_SOLOPT(cginfo_mb[mb].cginfo[i], bestsol);
+ fr->nWatMol += nmol;
+ }
+ else
+ {
+ SET_CGINFO_SOLOPT(cginfo_mb[mb].cginfo[i], esolNO);
+ }
+ }
+ sfree(cg_sp[mb]);
+ }
+ sfree(cg_sp);
+
+ if (bestsol != esolNO && fp != NULL)
+ {
+ fprintf(fp, "\nEnabling %s-like water optimization for %d molecules.\n\n",
+ esol_names[bestsol],
+ solvent_parameters[bestsp].count);
+ }
+
+ sfree(solvent_parameters);
+ fr->solvent_opt = bestsol;
+}
+
+enum {
+ acNONE = 0, acCONSTRAINT, acSETTLE
+};
+
+static cginfo_mb_t *init_cginfo_mb(FILE *fplog, const gmx_mtop_t *mtop,
+ t_forcerec *fr, gmx_bool bNoSolvOpt,
+ gmx_bool *bFEP_NonBonded,
+ gmx_bool *bExcl_IntraCGAll_InterCGNone)
+{
+ const t_block *cgs;
+ const t_blocka *excl;
+ const gmx_moltype_t *molt;
+ const gmx_molblock_t *molb;
+ cginfo_mb_t *cginfo_mb;
+ gmx_bool *type_VDW;
+ int *cginfo;
+ int cg_offset, a_offset, cgm, am;
+ int mb, m, ncg_tot, cg, a0, a1, gid, ai, j, aj, excl_nalloc;
+ int *a_con;
+ int ftype;
+ int ia;
+ gmx_bool bId, *bExcl, bExclIntraAll, bExclInter, bHaveVDW, bHaveQ, bHavePerturbedAtoms;
+
+ ncg_tot = ncg_mtop(mtop);
+ snew(cginfo_mb, mtop->nmolblock);
+
+ snew(type_VDW, fr->ntype);
+ for (ai = 0; ai < fr->ntype; ai++)
+ {
+ type_VDW[ai] = FALSE;
+ for (j = 0; j < fr->ntype; j++)
+ {
+ type_VDW[ai] = type_VDW[ai] ||
+ fr->bBHAM ||
+ C6(fr->nbfp, fr->ntype, ai, j) != 0 ||
+ C12(fr->nbfp, fr->ntype, ai, j) != 0;
+ }
+ }
+
+ *bFEP_NonBonded = FALSE;
+ *bExcl_IntraCGAll_InterCGNone = TRUE;
+
+ excl_nalloc = 10;
+ snew(bExcl, excl_nalloc);
+ cg_offset = 0;
+ a_offset = 0;
+ for (mb = 0; mb < mtop->nmolblock; mb++)
+ {
+ molb = &mtop->molblock[mb];
+ molt = &mtop->moltype[molb->type];
+ cgs = &molt->cgs;
+ excl = &molt->excls;
+
+ /* Check if the cginfo is identical for all molecules in this block.
+ * If so, we only need an array of the size of one molecule.
+ * Otherwise we make an array of #mol times #cgs per molecule.
+ */
+ bId = TRUE;
+ am = 0;
+ for (m = 0; m < molb->nmol; m++)
+ {
+ am = m*cgs->index[cgs->nr];
+ for (cg = 0; cg < cgs->nr; cg++)
+ {
+ a0 = cgs->index[cg];
+ a1 = cgs->index[cg+1];
+ if (ggrpnr(&mtop->groups, egcENER, a_offset+am+a0) !=
+ ggrpnr(&mtop->groups, egcENER, a_offset +a0))
+ {
+ bId = FALSE;
+ }
+ if (mtop->groups.grpnr[egcQMMM] != NULL)
+ {
+ for (ai = a0; ai < a1; ai++)
+ {
+ if (mtop->groups.grpnr[egcQMMM][a_offset+am+ai] !=
+ mtop->groups.grpnr[egcQMMM][a_offset +ai])
+ {
+ bId = FALSE;
+ }
+ }
+ }
+ }
+ }
+
+ cginfo_mb[mb].cg_start = cg_offset;
+ cginfo_mb[mb].cg_end = cg_offset + molb->nmol*cgs->nr;
+ cginfo_mb[mb].cg_mod = (bId ? 1 : molb->nmol)*cgs->nr;
+ snew(cginfo_mb[mb].cginfo, cginfo_mb[mb].cg_mod);
+ cginfo = cginfo_mb[mb].cginfo;
+
+ /* Set constraints flags for constrained atoms */
+ snew(a_con, molt->atoms.nr);
+ for (ftype = 0; ftype < F_NRE; ftype++)
+ {
+ if (interaction_function[ftype].flags & IF_CONSTRAINT)
+ {
+ int nral;
+
+ nral = NRAL(ftype);
+ for (ia = 0; ia < molt->ilist[ftype].nr; ia += 1+nral)
+ {
+ int a;
+
+ for (a = 0; a < nral; a++)
+ {
+ a_con[molt->ilist[ftype].iatoms[ia+1+a]] =
+ (ftype == F_SETTLE ? acSETTLE : acCONSTRAINT);
+ }
+ }
+ }
+ }
+
+ for (m = 0; m < (bId ? 1 : molb->nmol); m++)
+ {
+ cgm = m*cgs->nr;
+ am = m*cgs->index[cgs->nr];
+ for (cg = 0; cg < cgs->nr; cg++)
+ {
+ a0 = cgs->index[cg];
+ a1 = cgs->index[cg+1];
+
+ /* Store the energy group in cginfo */
+ gid = ggrpnr(&mtop->groups, egcENER, a_offset+am+a0);
+ SET_CGINFO_GID(cginfo[cgm+cg], gid);
+
+ /* Check the intra/inter charge group exclusions */
+ if (a1-a0 > excl_nalloc)
+ {
+ excl_nalloc = a1 - a0;
+ srenew(bExcl, excl_nalloc);
+ }
+ /* bExclIntraAll: all intra cg interactions excluded
+ * bExclInter: any inter cg interactions excluded
+ */
+ bExclIntraAll = TRUE;
+ bExclInter = FALSE;
+ bHaveVDW = FALSE;
+ bHaveQ = FALSE;
+ bHavePerturbedAtoms = FALSE;
+ for (ai = a0; ai < a1; ai++)
+ {
+ /* Check VDW and electrostatic interactions */
+ bHaveVDW = bHaveVDW || (type_VDW[molt->atoms.atom[ai].type] ||
+ type_VDW[molt->atoms.atom[ai].typeB]);
+ bHaveQ = bHaveQ || (molt->atoms.atom[ai].q != 0 ||
+ molt->atoms.atom[ai].qB != 0);
+
+ bHavePerturbedAtoms = bHavePerturbedAtoms || (PERTURBED(molt->atoms.atom[ai]) != 0);
+
+ /* Clear the exclusion list for atom ai */
+ for (aj = a0; aj < a1; aj++)
+ {
+ bExcl[aj-a0] = FALSE;
+ }
+ /* Loop over all the exclusions of atom ai */
+ for (j = excl->index[ai]; j < excl->index[ai+1]; j++)
+ {
+ aj = excl->a[j];
+ if (aj < a0 || aj >= a1)
+ {
+ bExclInter = TRUE;
+ }
+ else
+ {
+ bExcl[aj-a0] = TRUE;
+ }
+ }
+ /* Check if ai excludes a0 to a1 */
+ for (aj = a0; aj < a1; aj++)
+ {
+ if (!bExcl[aj-a0])
+ {
+ bExclIntraAll = FALSE;
+ }
+ }
+
+ switch (a_con[ai])
+ {
+ case acCONSTRAINT:
+ SET_CGINFO_CONSTR(cginfo[cgm+cg]);
+ break;
+ case acSETTLE:
+ SET_CGINFO_SETTLE(cginfo[cgm+cg]);
+ break;
+ default:
+ break;
+ }
+ }
+ if (bExclIntraAll)
+ {
+ SET_CGINFO_EXCL_INTRA(cginfo[cgm+cg]);
+ }
+ if (bExclInter)
+ {
+ SET_CGINFO_EXCL_INTER(cginfo[cgm+cg]);
+ }
+ if (a1 - a0 > MAX_CHARGEGROUP_SIZE)
+ {
+ /* The size in cginfo is currently only read with DD */
+ gmx_fatal(FARGS, "A charge group has size %d which is larger than the limit of %d atoms", a1-a0, MAX_CHARGEGROUP_SIZE);
+ }
+ if (bHaveVDW)
+ {
+ SET_CGINFO_HAS_VDW(cginfo[cgm+cg]);
+ }
+ if (bHaveQ)
+ {
+ SET_CGINFO_HAS_Q(cginfo[cgm+cg]);
+ }
+ if (bHavePerturbedAtoms && fr->efep != efepNO)
+ {
+ SET_CGINFO_FEP(cginfo[cgm+cg]);
+ *bFEP_NonBonded = TRUE;
+ }
+ /* Store the charge group size */
+ SET_CGINFO_NATOMS(cginfo[cgm+cg], a1-a0);
+
+ if (!bExclIntraAll || bExclInter)
+ {
+ *bExcl_IntraCGAll_InterCGNone = FALSE;
+ }
+ }
+ }
+
+ sfree(a_con);
+
+ cg_offset += molb->nmol*cgs->nr;
+ a_offset += molb->nmol*cgs->index[cgs->nr];
+ }
+ sfree(bExcl);
+
+ /* the solvent optimizer is called after the QM is initialized,
+ * because we don't want to have the QM subsystemto become an
+ * optimized solvent
+ */
+
+ check_solvent(fplog, mtop, fr, cginfo_mb);
+
+ if (getenv("GMX_NO_SOLV_OPT"))
+ {
+ if (fplog)
+ {
+ fprintf(fplog, "Found environment variable GMX_NO_SOLV_OPT.\n"
+ "Disabling all solvent optimization\n");
+ }
+ fr->solvent_opt = esolNO;
+ }
+ if (bNoSolvOpt)
+ {
+ fr->solvent_opt = esolNO;
+ }
+ if (!fr->solvent_opt)
+ {
+ for (mb = 0; mb < mtop->nmolblock; mb++)
+ {
+ for (cg = 0; cg < cginfo_mb[mb].cg_mod; cg++)
+ {
+ SET_CGINFO_SOLOPT(cginfo_mb[mb].cginfo[cg], esolNO);
+ }
+ }
+ }
+
+ return cginfo_mb;
+}
+
+static int *cginfo_expand(int nmb, cginfo_mb_t *cgi_mb)
+{
+ int ncg, mb, cg;
+ int *cginfo;
+
+ ncg = cgi_mb[nmb-1].cg_end;
+ snew(cginfo, ncg);
+ mb = 0;
+ for (cg = 0; cg < ncg; cg++)
+ {
+ while (cg >= cgi_mb[mb].cg_end)
+ {
+ mb++;
+ }
+ cginfo[cg] =
+ cgi_mb[mb].cginfo[(cg - cgi_mb[mb].cg_start) % cgi_mb[mb].cg_mod];
+ }
+
+ return cginfo;
+}
+
+static void set_chargesum(FILE *log, t_forcerec *fr, const gmx_mtop_t *mtop)
+{
+ /*This now calculates sum for q and c6*/
+ double qsum, q2sum, q, c6sum, c6;
+ int mb, nmol, i;
+ const t_atoms *atoms;
+
+ qsum = 0;
+ q2sum = 0;
+ c6sum = 0;
+ for (mb = 0; mb < mtop->nmolblock; mb++)
+ {
+ nmol = mtop->molblock[mb].nmol;
+ atoms = &mtop->moltype[mtop->molblock[mb].type].atoms;
+ for (i = 0; i < atoms->nr; i++)
+ {
+ q = atoms->atom[i].q;
+ qsum += nmol*q;
+ q2sum += nmol*q*q;
+ c6 = mtop->ffparams.iparams[atoms->atom[i].type*(mtop->ffparams.atnr+1)].lj.c6;
+ c6sum += nmol*c6;
+ }
+ }
+ fr->qsum[0] = qsum;
+ fr->q2sum[0] = q2sum;
+ fr->c6sum[0] = c6sum;
+
+ if (fr->efep != efepNO)
+ {
+ qsum = 0;
+ q2sum = 0;
+ c6sum = 0;
+ for (mb = 0; mb < mtop->nmolblock; mb++)
+ {
+ nmol = mtop->molblock[mb].nmol;
+ atoms = &mtop->moltype[mtop->molblock[mb].type].atoms;
+ for (i = 0; i < atoms->nr; i++)
+ {
+ q = atoms->atom[i].qB;
+ qsum += nmol*q;
+ q2sum += nmol*q*q;
+ c6 = mtop->ffparams.iparams[atoms->atom[i].typeB*(mtop->ffparams.atnr+1)].lj.c6;
+ c6sum += nmol*c6;
+ }
+ fr->qsum[1] = qsum;
+ fr->q2sum[1] = q2sum;
+ fr->c6sum[1] = c6sum;
+ }
+ }
+ else
+ {
+ fr->qsum[1] = fr->qsum[0];
+ fr->q2sum[1] = fr->q2sum[0];
+ fr->c6sum[1] = fr->c6sum[0];
+ }
+ if (log)
+ {
+ if (fr->efep == efepNO)
+ {
+ fprintf(log, "System total charge: %.3f\n", fr->qsum[0]);
+ }
+ else
+ {
+ fprintf(log, "System total charge, top. A: %.3f top. B: %.3f\n",
+ fr->qsum[0], fr->qsum[1]);
+ }
+ }
+}
+
+void update_forcerec(t_forcerec *fr, matrix box)
+{
+ if (fr->eeltype == eelGRF)
+ {
+ calc_rffac(NULL, fr->eeltype, fr->epsilon_r, fr->epsilon_rf,
+ fr->rcoulomb, fr->temp, fr->zsquare, box,
+ &fr->kappa, &fr->k_rf, &fr->c_rf);
+ }
+}
+
+void set_avcsixtwelve(FILE *fplog, t_forcerec *fr, const gmx_mtop_t *mtop)
+{
+ const t_atoms *atoms, *atoms_tpi;
+ const t_blocka *excl;
+ int mb, nmol, nmolc, i, j, tpi, tpj, j1, j2, k, n, nexcl, q;
+ gmx_int64_t npair, npair_ij, tmpi, tmpj;
+ double csix, ctwelve;
+ int ntp, *typecount;
+ gmx_bool bBHAM;
+ real *nbfp;
+ real *nbfp_comb = NULL;
+
+ ntp = fr->ntype;
+ bBHAM = fr->bBHAM;
+ nbfp = fr->nbfp;
+
+ /* For LJ-PME, we want to correct for the difference between the
+ * actual C6 values and the C6 values used by the LJ-PME based on
+ * combination rules. */
+
+ if (EVDW_PME(fr->vdwtype))
+ {
+ nbfp_comb = mk_nbfp_combination_rule(&mtop->ffparams,
+ (fr->ljpme_combination_rule == eljpmeLB) ? eCOMB_ARITHMETIC : eCOMB_GEOMETRIC);
+ for (tpi = 0; tpi < ntp; ++tpi)
+ {
+ for (tpj = 0; tpj < ntp; ++tpj)
+ {
+ C6(nbfp_comb, ntp, tpi, tpj) =
+ C6(nbfp, ntp, tpi, tpj) - C6(nbfp_comb, ntp, tpi, tpj);
+ C12(nbfp_comb, ntp, tpi, tpj) = C12(nbfp, ntp, tpi, tpj);
+ }
+ }
+ nbfp = nbfp_comb;
+ }
+ for (q = 0; q < (fr->efep == efepNO ? 1 : 2); q++)
+ {
+ csix = 0;
+ ctwelve = 0;
+ npair = 0;
+ nexcl = 0;
+ if (!fr->n_tpi)
+ {
+ /* Count the types so we avoid natoms^2 operations */
+ snew(typecount, ntp);
+ gmx_mtop_count_atomtypes(mtop, q, typecount);
+
+ for (tpi = 0; tpi < ntp; tpi++)
+ {
+ for (tpj = tpi; tpj < ntp; tpj++)
+ {
+ tmpi = typecount[tpi];
+ tmpj = typecount[tpj];
+ if (tpi != tpj)
+ {
+ npair_ij = tmpi*tmpj;
+ }
+ else
+ {
+ npair_ij = tmpi*(tmpi - 1)/2;
+ }
+ if (bBHAM)
+ {
+ /* nbfp now includes the 6.0 derivative prefactor */
+ csix += npair_ij*BHAMC(nbfp, ntp, tpi, tpj)/6.0;
+ }
+ else
+ {
+ /* nbfp now includes the 6.0/12.0 derivative prefactors */
+ csix += npair_ij* C6(nbfp, ntp, tpi, tpj)/6.0;
+ ctwelve += npair_ij* C12(nbfp, ntp, tpi, tpj)/12.0;
+ }
+ npair += npair_ij;
+ }
+ }
+ sfree(typecount);
+ /* Subtract the excluded pairs.
+ * The main reason for substracting exclusions is that in some cases
+ * some combinations might never occur and the parameters could have
+ * any value. These unused values should not influence the dispersion
+ * correction.
+ */
+ for (mb = 0; mb < mtop->nmolblock; mb++)
+ {
+ nmol = mtop->molblock[mb].nmol;
+ atoms = &mtop->moltype[mtop->molblock[mb].type].atoms;
+ excl = &mtop->moltype[mtop->molblock[mb].type].excls;
+ for (i = 0; (i < atoms->nr); i++)
+ {
+ if (q == 0)
+ {
+ tpi = atoms->atom[i].type;
+ }
+ else
+ {
+ tpi = atoms->atom[i].typeB;
+ }
+ j1 = excl->index[i];
+ j2 = excl->index[i+1];
+ for (j = j1; j < j2; j++)
+ {
+ k = excl->a[j];
+ if (k > i)
+ {
+ if (q == 0)
+ {
+ tpj = atoms->atom[k].type;
+ }
+ else
+ {
+ tpj = atoms->atom[k].typeB;
+ }
+ if (bBHAM)
+ {
+ /* nbfp now includes the 6.0 derivative prefactor */
+ csix -= nmol*BHAMC(nbfp, ntp, tpi, tpj)/6.0;
+ }
+ else
+ {
+ /* nbfp now includes the 6.0/12.0 derivative prefactors */
+ csix -= nmol*C6 (nbfp, ntp, tpi, tpj)/6.0;
+ ctwelve -= nmol*C12(nbfp, ntp, tpi, tpj)/12.0;
+ }
+ nexcl += nmol;
+ }
+ }
+ }
+ }
+ }
+ else
+ {
+ /* Only correct for the interaction of the test particle
+ * with the rest of the system.
+ */
+ atoms_tpi =
+ &mtop->moltype[mtop->molblock[mtop->nmolblock-1].type].atoms;
+
+ npair = 0;
+ for (mb = 0; mb < mtop->nmolblock; mb++)
+ {
+ nmol = mtop->molblock[mb].nmol;
+ atoms = &mtop->moltype[mtop->molblock[mb].type].atoms;
+ for (j = 0; j < atoms->nr; j++)
+ {
+ nmolc = nmol;
+ /* Remove the interaction of the test charge group
+ * with itself.
+ */
+ if (mb == mtop->nmolblock-1)
+ {
+ nmolc--;
+
+ if (mb == 0 && nmol == 1)
+ {
+ gmx_fatal(FARGS, "Old format tpr with TPI, please generate a new tpr file");
+ }
+ }
+ if (q == 0)
+ {
+ tpj = atoms->atom[j].type;
+ }
+ else
+ {
+ tpj = atoms->atom[j].typeB;
+ }
+ for (i = 0; i < fr->n_tpi; i++)
+ {
+ if (q == 0)
+ {
+ tpi = atoms_tpi->atom[i].type;
+ }
+ else
+ {
+ tpi = atoms_tpi->atom[i].typeB;
+ }
+ if (bBHAM)
+ {
+ /* nbfp now includes the 6.0 derivative prefactor */
+ csix += nmolc*BHAMC(nbfp, ntp, tpi, tpj)/6.0;
+ }
+ else
+ {
+ /* nbfp now includes the 6.0/12.0 derivative prefactors */
+ csix += nmolc*C6 (nbfp, ntp, tpi, tpj)/6.0;
+ ctwelve += nmolc*C12(nbfp, ntp, tpi, tpj)/12.0;
+ }
+ npair += nmolc;
+ }
+ }
+ }
+ }
+ if (npair - nexcl <= 0 && fplog)
+ {
+ fprintf(fplog, "\nWARNING: There are no atom pairs for dispersion correction\n\n");
+ csix = 0;
+ ctwelve = 0;
+ }
+ else
+ {
+ csix /= npair - nexcl;
+ ctwelve /= npair - nexcl;
+ }
+ if (debug)
+ {
+ fprintf(debug, "Counted %d exclusions\n", nexcl);
+ fprintf(debug, "Average C6 parameter is: %10g\n", (double)csix);
+ fprintf(debug, "Average C12 parameter is: %10g\n", (double)ctwelve);
+ }
+ fr->avcsix[q] = csix;
+ fr->avctwelve[q] = ctwelve;
+ }
+
+ if (EVDW_PME(fr->vdwtype))
+ {
+ sfree(nbfp_comb);
+ }
+
+ if (fplog != NULL)
+ {
+ if (fr->eDispCorr == edispcAllEner ||
+ fr->eDispCorr == edispcAllEnerPres)
+ {
+ fprintf(fplog, "Long Range LJ corr.: <C6> %10.4e, <C12> %10.4e\n",
+ fr->avcsix[0], fr->avctwelve[0]);
+ }
+ else
+ {
+ fprintf(fplog, "Long Range LJ corr.: <C6> %10.4e\n", fr->avcsix[0]);
+ }
+ }
+}
+
+
+static void set_bham_b_max(FILE *fplog, t_forcerec *fr,
+ const gmx_mtop_t *mtop)
+{
+ const t_atoms *at1, *at2;
+ int mt1, mt2, i, j, tpi, tpj, ntypes;
+ real b, bmin;
+ real *nbfp;
+
+ if (fplog)
+ {
+ fprintf(fplog, "Determining largest Buckingham b parameter for table\n");
+ }
+ nbfp = fr->nbfp;
+ ntypes = fr->ntype;
+
+ bmin = -1;
+ fr->bham_b_max = 0;
+ for (mt1 = 0; mt1 < mtop->nmoltype; mt1++)
+ {
+ at1 = &mtop->moltype[mt1].atoms;
+ for (i = 0; (i < at1->nr); i++)
+ {
+ tpi = at1->atom[i].type;
+ if (tpi >= ntypes)
+ {
+ gmx_fatal(FARGS, "Atomtype[%d] = %d, maximum = %d", i, tpi, ntypes);
+ }
+
+ for (mt2 = mt1; mt2 < mtop->nmoltype; mt2++)
+ {
+ at2 = &mtop->moltype[mt2].atoms;
+ for (j = 0; (j < at2->nr); j++)
+ {
+ tpj = at2->atom[j].type;
+ if (tpj >= ntypes)
+ {
+ gmx_fatal(FARGS, "Atomtype[%d] = %d, maximum = %d", j, tpj, ntypes);
+ }
+ b = BHAMB(nbfp, ntypes, tpi, tpj);
+ if (b > fr->bham_b_max)
+ {
+ fr->bham_b_max = b;
+ }
+ if ((b < bmin) || (bmin == -1))
+ {
+ bmin = b;
+ }
+ }
+ }
+ }
+ }
+ if (fplog)
+ {
+ fprintf(fplog, "Buckingham b parameters, min: %g, max: %g\n",
+ bmin, fr->bham_b_max);
+ }
+}
+
+static void make_nbf_tables(FILE *fp, const output_env_t oenv,
+ t_forcerec *fr, real rtab,
+ const t_commrec *cr,
+ const char *tabfn, char *eg1, char *eg2,
+ t_nblists *nbl)
+{
+ char buf[STRLEN];
+ int i, j;
+
+ if (tabfn == NULL)
+ {
+ if (debug)
+ {
+ fprintf(debug, "No table file name passed, can not read table, can not do non-bonded interactions\n");
+ }
+ return;
+ }
+
+ sprintf(buf, "%s", tabfn);
+ if (eg1 && eg2)
+ {
+ /* Append the two energy group names */
+ sprintf(buf + strlen(tabfn) - strlen(ftp2ext(efXVG)) - 1, "_%s_%s.%s",
+ eg1, eg2, ftp2ext(efXVG));
+ }
+ nbl->table_elec_vdw = make_tables(fp, oenv, fr, MASTER(cr), buf, rtab, 0);
+ /* Copy the contents of the table to separate coulomb and LJ tables too,
+ * to improve cache performance.
+ */
+ /* For performance reasons we want
+ * the table data to be aligned to 16-byte. The pointers could be freed
+ * but currently aren't.
+ */
+ nbl->table_elec.interaction = GMX_TABLE_INTERACTION_ELEC;
+ nbl->table_elec.format = nbl->table_elec_vdw.format;
+ nbl->table_elec.r = nbl->table_elec_vdw.r;
+ nbl->table_elec.n = nbl->table_elec_vdw.n;
+ nbl->table_elec.scale = nbl->table_elec_vdw.scale;
+ nbl->table_elec.scale_exp = nbl->table_elec_vdw.scale_exp;
+ nbl->table_elec.formatsize = nbl->table_elec_vdw.formatsize;
+ nbl->table_elec.ninteractions = 1;
+ nbl->table_elec.stride = nbl->table_elec.formatsize * nbl->table_elec.ninteractions;
+ snew_aligned(nbl->table_elec.data, nbl->table_elec.stride*(nbl->table_elec.n+1), 32);
+
+ nbl->table_vdw.interaction = GMX_TABLE_INTERACTION_VDWREP_VDWDISP;
+ nbl->table_vdw.format = nbl->table_elec_vdw.format;
+ nbl->table_vdw.r = nbl->table_elec_vdw.r;
+ nbl->table_vdw.n = nbl->table_elec_vdw.n;
+ nbl->table_vdw.scale = nbl->table_elec_vdw.scale;
+ nbl->table_vdw.scale_exp = nbl->table_elec_vdw.scale_exp;
+ nbl->table_vdw.formatsize = nbl->table_elec_vdw.formatsize;
+ nbl->table_vdw.ninteractions = 2;
+ nbl->table_vdw.stride = nbl->table_vdw.formatsize * nbl->table_vdw.ninteractions;
+ snew_aligned(nbl->table_vdw.data, nbl->table_vdw.stride*(nbl->table_vdw.n+1), 32);
+
+ for (i = 0; i <= nbl->table_elec_vdw.n; i++)
+ {
+ for (j = 0; j < 4; j++)
+ {
+ nbl->table_elec.data[4*i+j] = nbl->table_elec_vdw.data[12*i+j];
+ }
+ for (j = 0; j < 8; j++)
+ {
+ nbl->table_vdw.data[8*i+j] = nbl->table_elec_vdw.data[12*i+4+j];
+ }
+ }
+}
+
+static void count_tables(int ftype1, int ftype2, const gmx_mtop_t *mtop,
+ int *ncount, int **count)
+{
+ const gmx_moltype_t *molt;
+ const t_ilist *il;
+ int mt, ftype, stride, i, j, tabnr;
+
+ for (mt = 0; mt < mtop->nmoltype; mt++)
+ {
+ molt = &mtop->moltype[mt];
+ for (ftype = 0; ftype < F_NRE; ftype++)
+ {
+ if (ftype == ftype1 || ftype == ftype2)
+ {
+ il = &molt->ilist[ftype];
+ stride = 1 + NRAL(ftype);
+ for (i = 0; i < il->nr; i += stride)
+ {
+ tabnr = mtop->ffparams.iparams[il->iatoms[i]].tab.table;
+ if (tabnr < 0)
+ {
+ gmx_fatal(FARGS, "A bonded table number is smaller than 0: %d\n", tabnr);
+ }
+ if (tabnr >= *ncount)
+ {
+ srenew(*count, tabnr+1);
+ for (j = *ncount; j < tabnr+1; j++)
+ {
+ (*count)[j] = 0;
+ }
+ *ncount = tabnr+1;
+ }
+ (*count)[tabnr]++;
+ }
+ }
+ }
+ }
+}
+
+static bondedtable_t *make_bonded_tables(FILE *fplog,
+ int ftype1, int ftype2,
+ const gmx_mtop_t *mtop,
+ const char *basefn, const char *tabext)
+{
+ int i, ncount, *count;
+ char tabfn[STRLEN];
+ bondedtable_t *tab;
+
+ tab = NULL;
+
+ ncount = 0;
+ count = NULL;
+ count_tables(ftype1, ftype2, mtop, &ncount, &count);
+
+ if (ncount > 0)
+ {
+ snew(tab, ncount);
+ for (i = 0; i < ncount; i++)
+ {
+ if (count[i] > 0)
+ {
+ sprintf(tabfn, "%s", basefn);
+ sprintf(tabfn + strlen(basefn) - strlen(ftp2ext(efXVG)) - 1, "_%s%d.%s",
+ tabext, i, ftp2ext(efXVG));
+ tab[i] = make_bonded_table(fplog, tabfn, NRAL(ftype1)-2);
+ }
+ }
+ sfree(count);
+ }
+
+ return tab;
+}
+
+void forcerec_set_ranges(t_forcerec *fr,
+ int ncg_home, int ncg_force,
+ int natoms_force,
+ int natoms_force_constr, int natoms_f_novirsum)
+{
+ fr->cg0 = 0;
+ fr->hcg = ncg_home;
+
+ /* fr->ncg_force is unused in the standard code,
+ * but it can be useful for modified code dealing with charge groups.
+ */
+ fr->ncg_force = ncg_force;
+ fr->natoms_force = natoms_force;
+ fr->natoms_force_constr = natoms_force_constr;
+
+ if (fr->natoms_force_constr > fr->nalloc_force)
+ {
+ fr->nalloc_force = over_alloc_dd(fr->natoms_force_constr);
+
+ if (fr->bTwinRange)
+ {
+ srenew(fr->f_twin, fr->nalloc_force);
+ }
+ }
+
+ if (fr->bF_NoVirSum)
+ {
+ fr->f_novirsum_n = natoms_f_novirsum;
+ if (fr->f_novirsum_n > fr->f_novirsum_nalloc)
+ {
+ fr->f_novirsum_nalloc = over_alloc_dd(fr->f_novirsum_n);
+ srenew(fr->f_novirsum_alloc, fr->f_novirsum_nalloc);
+ }
+ }
+ else
+ {
+ fr->f_novirsum_n = 0;
+ }
+}
+
+static real cutoff_inf(real cutoff)
+{
+ if (cutoff == 0)
+ {
+ cutoff = GMX_CUTOFF_INF;
+ }
+
+ return cutoff;
+}
+
+static void make_adress_tf_tables(FILE *fp, const output_env_t oenv,
+ t_forcerec *fr, const t_inputrec *ir,
+ const char *tabfn, const gmx_mtop_t *mtop,
+ matrix box)
+{
+ char buf[STRLEN];
+ int i, j;
+
+ if (tabfn == NULL)
+ {
+ gmx_fatal(FARGS, "No thermoforce table file given. Use -tabletf to specify a file\n");
+ return;
+ }
+
+ snew(fr->atf_tabs, ir->adress->n_tf_grps);
+
+ sprintf(buf, "%s", tabfn);
+ for (i = 0; i < ir->adress->n_tf_grps; i++)
+ {
+ j = ir->adress->tf_table_index[i]; /* get energy group index */
+ sprintf(buf + strlen(tabfn) - strlen(ftp2ext(efXVG)) - 1, "tf_%s.%s",
+ *(mtop->groups.grpname[mtop->groups.grps[egcENER].nm_ind[j]]), ftp2ext(efXVG));
+ if (fp)
+ {
+ fprintf(fp, "loading tf table for energygrp index %d from %s\n", ir->adress->tf_table_index[i], buf);
+ }
+ fr->atf_tabs[i] = make_atf_table(fp, oenv, fr, buf, box);
+ }
+
+}
+
+gmx_bool can_use_allvsall(const t_inputrec *ir, gmx_bool bPrintNote, t_commrec *cr, FILE *fp)
+{
+ gmx_bool bAllvsAll;
+
+ bAllvsAll =
+ (
+ ir->rlist == 0 &&
+ ir->rcoulomb == 0 &&
+ ir->rvdw == 0 &&
+ ir->ePBC == epbcNONE &&
+ ir->vdwtype == evdwCUT &&
+ ir->coulombtype == eelCUT &&
+ ir->efep == efepNO &&
+ (ir->implicit_solvent == eisNO ||
+ (ir->implicit_solvent == eisGBSA && (ir->gb_algorithm == egbSTILL ||
+ ir->gb_algorithm == egbHCT ||
+ ir->gb_algorithm == egbOBC))) &&
+ getenv("GMX_NO_ALLVSALL") == NULL
+ );
+
+ if (bAllvsAll && ir->opts.ngener > 1)
+ {
+ const char *note = "NOTE: Can not use all-vs-all force loops, because there are multiple energy monitor groups; you might get significantly higher performance when using only a single energy monitor group.\n";
+
+ if (bPrintNote)
+ {
+ if (MASTER(cr))
+ {
+ fprintf(stderr, "\n%s\n", note);
+ }
+ if (fp != NULL)
+ {
+ fprintf(fp, "\n%s\n", note);
+ }
+ }
+ bAllvsAll = FALSE;
+ }
+
+ if (bAllvsAll && fp && MASTER(cr))
+ {
+ fprintf(fp, "\nUsing SIMD all-vs-all kernels.\n\n");
+ }
+
+ return bAllvsAll;
+}
+
+
+static void init_forcerec_f_threads(t_forcerec *fr, int nenergrp)
+{
+ int t, i;
+
+ /* These thread local data structures are used for bondeds only */
+ fr->nthreads = gmx_omp_nthreads_get(emntBonded);
+
+ if (fr->nthreads > 1)
+ {
+ snew(fr->f_t, fr->nthreads);
+ /* Thread 0 uses the global force and energy arrays */
+ for (t = 1; t < fr->nthreads; t++)
+ {
+ fr->f_t[t].f = NULL;
+ fr->f_t[t].f_nalloc = 0;
+ snew(fr->f_t[t].fshift, SHIFTS);
+ fr->f_t[t].grpp.nener = nenergrp*nenergrp;
+ for (i = 0; i < egNR; i++)
+ {
+ snew(fr->f_t[t].grpp.ener[i], fr->f_t[t].grpp.nener);
+ }
+ }
+ }
+}
+
+
+gmx_bool nbnxn_acceleration_supported(FILE *fplog,
+ const t_commrec *cr,
+ const t_inputrec *ir,
+ gmx_bool bGPU)
+{
+ if (!bGPU && (ir->vdwtype == evdwPME && ir->ljpme_combination_rule == eljpmeLB))
+ {
+ md_print_warn(cr, fplog, "LJ-PME with Lorentz-Berthelot is not supported with %s, falling back to %s\n",
+ bGPU ? "GPUs" : "SIMD kernels",
+ bGPU ? "CPU only" : "plain-C kernels");
+ return FALSE;
+ }
+
+ return TRUE;
+}
+
+
+static void pick_nbnxn_kernel_cpu(const t_inputrec gmx_unused *ir,
+ int *kernel_type,
+ int *ewald_excl)
+{
+ *kernel_type = nbnxnk4x4_PlainC;
+ *ewald_excl = ewaldexclTable;
+
+#ifdef GMX_NBNXN_SIMD
+ {
+#ifdef GMX_NBNXN_SIMD_4XN
+ *kernel_type = nbnxnk4xN_SIMD_4xN;
+#endif
+#ifdef GMX_NBNXN_SIMD_2XNN
+ *kernel_type = nbnxnk4xN_SIMD_2xNN;
+#endif
+
+#if defined GMX_NBNXN_SIMD_2XNN && defined GMX_NBNXN_SIMD_4XN
+ /* We need to choose if we want 2x(N+N) or 4xN kernels.
+ * Currently this is based on the SIMD acceleration choice,
+ * but it might be better to decide this at runtime based on CPU.
+ *
+ * 4xN calculates more (zero) interactions, but has less pair-search
+ * work and much better kernel instruction scheduling.
+ *
+ * Up till now we have only seen that on Intel Sandy/Ivy Bridge,
+ * which doesn't have FMA, both the analytical and tabulated Ewald
+ * kernels have similar pair rates for 4x8 and 2x(4+4), so we choose
+ * 2x(4+4) because it results in significantly fewer pairs.
+ * For RF, the raw pair rate of the 4x8 kernel is higher than 2x(4+4),
+ * 10% with HT, 50% without HT. As we currently don't detect the actual
+ * use of HT, use 4x8 to avoid a potential performance hit.
+ * On Intel Haswell 4x8 is always faster.
+ */
+ *kernel_type = nbnxnk4xN_SIMD_4xN;
+
+#ifndef GMX_SIMD_HAVE_FMA
+ if (EEL_PME_EWALD(ir->coulombtype) ||
+ EVDW_PME(ir->vdwtype))
+ {
+ /* We have Ewald kernels without FMA (Intel Sandy/Ivy Bridge).
+ * There are enough instructions to make 2x(4+4) efficient.
+ */
+ *kernel_type = nbnxnk4xN_SIMD_2xNN;
+ }
+#endif
+#endif /* GMX_NBNXN_SIMD_2XNN && GMX_NBNXN_SIMD_4XN */
+
+
+ if (getenv("GMX_NBNXN_SIMD_4XN") != NULL)
+ {
+#ifdef GMX_NBNXN_SIMD_4XN
+ *kernel_type = nbnxnk4xN_SIMD_4xN;
+#else
+ gmx_fatal(FARGS, "SIMD 4xN kernels requested, but Gromacs has been compiled without support for these kernels");
+#endif
+ }
+ if (getenv("GMX_NBNXN_SIMD_2XNN") != NULL)
+ {
+#ifdef GMX_NBNXN_SIMD_2XNN
+ *kernel_type = nbnxnk4xN_SIMD_2xNN;
+#else
+ gmx_fatal(FARGS, "SIMD 2x(N+N) kernels requested, but Gromacs has been compiled without support for these kernels");
+#endif
+ }
+
+ /* Analytical Ewald exclusion correction is only an option in
+ * the SIMD kernel.
+ * Since table lookup's don't parallelize with SIMD, analytical
+ * will probably always be faster for a SIMD width of 8 or more.
+ * With FMA analytical is sometimes faster for a width if 4 as well.
+ * On BlueGene/Q, this is faster regardless of precision.
+ * In single precision, this is faster on Bulldozer.
+ */
+#if GMX_SIMD_REAL_WIDTH >= 8 || \
+ (GMX_SIMD_REAL_WIDTH >= 4 && defined GMX_SIMD_HAVE_FMA && !defined GMX_DOUBLE) || \
+ defined GMX_SIMD_IBM_QPX
+ *ewald_excl = ewaldexclAnalytical;
+#endif
+ if (getenv("GMX_NBNXN_EWALD_TABLE") != NULL)
+ {
+ *ewald_excl = ewaldexclTable;
+ }
+ if (getenv("GMX_NBNXN_EWALD_ANALYTICAL") != NULL)
+ {
+ *ewald_excl = ewaldexclAnalytical;
+ }
+
+ }
+#endif /* GMX_NBNXN_SIMD */
+}
+
+
+const char *lookup_nbnxn_kernel_name(int kernel_type)
+{
+ const char *returnvalue = NULL;
+ switch (kernel_type)
+ {
+ case nbnxnkNotSet:
+ returnvalue = "not set";
+ break;
+ case nbnxnk4x4_PlainC:
+ returnvalue = "plain C";
+ break;
+ case nbnxnk4xN_SIMD_4xN:
+ case nbnxnk4xN_SIMD_2xNN:
+#ifdef GMX_NBNXN_SIMD
+#if defined GMX_SIMD_X86_SSE2
+ returnvalue = "SSE2";
+#elif defined GMX_SIMD_X86_SSE4_1
+ returnvalue = "SSE4.1";
+#elif defined GMX_SIMD_X86_AVX_128_FMA
+ returnvalue = "AVX_128_FMA";
+#elif defined GMX_SIMD_X86_AVX_256
+ returnvalue = "AVX_256";
+#elif defined GMX_SIMD_X86_AVX2_256
+ returnvalue = "AVX2_256";
+#else
+ returnvalue = "SIMD";
+#endif
+#else /* GMX_NBNXN_SIMD */
+ returnvalue = "not available";
+#endif /* GMX_NBNXN_SIMD */
+ break;
+ case nbnxnk8x8x8_CUDA: returnvalue = "CUDA"; break;
+ case nbnxnk8x8x8_PlainC: returnvalue = "plain C"; break;
+
+ case nbnxnkNR:
+ default:
+ gmx_fatal(FARGS, "Illegal kernel type selected");
+ returnvalue = NULL;
+ break;
+ }
+ return returnvalue;
+};
+
+static void pick_nbnxn_kernel(FILE *fp,
+ const t_commrec *cr,
+ gmx_bool use_simd_kernels,
+ gmx_bool bUseGPU,
+ gmx_bool bEmulateGPU,
+ const t_inputrec *ir,
+ int *kernel_type,
+ int *ewald_excl,
+ gmx_bool bDoNonbonded)
+{
+ assert(kernel_type);
+
+ *kernel_type = nbnxnkNotSet;
+ *ewald_excl = ewaldexclTable;
+
+ if (bEmulateGPU)
+ {
+ *kernel_type = nbnxnk8x8x8_PlainC;
+
+ if (bDoNonbonded)
+ {
+ md_print_warn(cr, fp, "Emulating a GPU run on the CPU (slow)");
+ }
+ }
+ else if (bUseGPU)
+ {
+ *kernel_type = nbnxnk8x8x8_CUDA;
+ }
+
+ if (*kernel_type == nbnxnkNotSet)
+ {
+ /* LJ PME with LB combination rule does 7 mesh operations.
+ * This so slow that we don't compile SIMD non-bonded kernels for that.
+ */
+ if (use_simd_kernels &&
+ nbnxn_acceleration_supported(fp, cr, ir, FALSE))
+ {
+ pick_nbnxn_kernel_cpu(ir, kernel_type, ewald_excl);
+ }
+ else
+ {
+ *kernel_type = nbnxnk4x4_PlainC;
+ }
+ }
+
+ if (bDoNonbonded && fp != NULL)
+ {
+ fprintf(fp, "\nUsing %s %dx%d non-bonded kernels\n\n",
+ lookup_nbnxn_kernel_name(*kernel_type),
+ nbnxn_kernel_pairlist_simple(*kernel_type) ? NBNXN_CPU_CLUSTER_I_SIZE : NBNXN_GPU_CLUSTER_SIZE,
+ nbnxn_kernel_to_cj_size(*kernel_type));
+ }
+}
+
+static void pick_nbnxn_resources(const t_commrec *cr,
+ const gmx_hw_info_t *hwinfo,
+ gmx_bool bDoNonbonded,
+ gmx_bool *bUseGPU,
+ gmx_bool *bEmulateGPU,
+ const gmx_gpu_opt_t *gpu_opt)
+{
+ gmx_bool bEmulateGPUEnvVarSet;
+ char gpu_err_str[STRLEN];
+
+ *bUseGPU = FALSE;
+
+ bEmulateGPUEnvVarSet = (getenv("GMX_EMULATE_GPU") != NULL);
+
+ /* Run GPU emulation mode if GMX_EMULATE_GPU is defined. Because
+ * GPUs (currently) only handle non-bonded calculations, we will
+ * automatically switch to emulation if non-bonded calculations are
+ * turned off via GMX_NO_NONBONDED - this is the simple and elegant
+ * way to turn off GPU initialization, data movement, and cleanup.
+ *
+ * GPU emulation can be useful to assess the performance one can expect by
+ * adding GPU(s) to the machine. The conditional below allows this even
+ * if mdrun is compiled without GPU acceleration support.
+ * Note that you should freezing the system as otherwise it will explode.
+ */
+ *bEmulateGPU = (bEmulateGPUEnvVarSet ||
+ (!bDoNonbonded &&
+ gpu_opt->ncuda_dev_use > 0));
+
+ /* Enable GPU mode when GPUs are available or no GPU emulation is requested.
+ */
+ if (gpu_opt->ncuda_dev_use > 0 && !(*bEmulateGPU))
+ {
+ /* Each PP node will use the intra-node id-th device from the
+ * list of detected/selected GPUs. */
+ if (!init_gpu(cr->rank_pp_intranode, gpu_err_str,
+ &hwinfo->gpu_info, gpu_opt))
+ {
+ /* At this point the init should never fail as we made sure that
+ * we have all the GPUs we need. If it still does, we'll bail. */
+ gmx_fatal(FARGS, "On node %d failed to initialize GPU #%d: %s",
+ cr->nodeid,
+ get_gpu_device_id(&hwinfo->gpu_info, gpu_opt,
+ cr->rank_pp_intranode),
+ gpu_err_str);
+ }
+
+ /* Here we actually turn on hardware GPU acceleration */
+ *bUseGPU = TRUE;
+ }
+}
+
+gmx_bool uses_simple_tables(int cutoff_scheme,
+ nonbonded_verlet_t *nbv,
+ int group)
+{
+ gmx_bool bUsesSimpleTables = TRUE;
+ int grp_index;
+
+ switch (cutoff_scheme)
+ {
+ case ecutsGROUP:
+ bUsesSimpleTables = TRUE;
+ break;
+ case ecutsVERLET:
+ assert(NULL != nbv && NULL != nbv->grp);
+ grp_index = (group < 0) ? 0 : (nbv->ngrp - 1);
+ bUsesSimpleTables = nbnxn_kernel_pairlist_simple(nbv->grp[grp_index].kernel_type);
+ break;
+ default:
+ gmx_incons("unimplemented");
+ }
+ return bUsesSimpleTables;
+}
+
+static void init_ewald_f_table(interaction_const_t *ic,
+ gmx_bool bUsesSimpleTables,
+ real rtab)
+{
+ real maxr;
+
+ if (bUsesSimpleTables)
+ {
+ /* With a spacing of 0.0005 we are at the force summation accuracy
+ * for the SSE kernels for "normal" atomistic simulations.
+ */
+ ic->tabq_scale = ewald_spline3_table_scale(ic->ewaldcoeff_q,
+ ic->rcoulomb);
+
+ maxr = (rtab > ic->rcoulomb) ? rtab : ic->rcoulomb;
+ ic->tabq_size = (int)(maxr*ic->tabq_scale) + 2;
+ }
+ else
+ {
+ ic->tabq_size = GPU_EWALD_COULOMB_FORCE_TABLE_SIZE;
+ /* Subtract 2 iso 1 to avoid access out of range due to rounding */
+ ic->tabq_scale = (ic->tabq_size - 2)/ic->rcoulomb;
+ }
+
+ sfree_aligned(ic->tabq_coul_FDV0);
+ sfree_aligned(ic->tabq_coul_F);
+ sfree_aligned(ic->tabq_coul_V);
+
+ sfree_aligned(ic->tabq_vdw_FDV0);
+ sfree_aligned(ic->tabq_vdw_F);
+ sfree_aligned(ic->tabq_vdw_V);
+
+ if (ic->eeltype == eelEWALD || EEL_PME(ic->eeltype))
+ {
+ /* Create the original table data in FDV0 */
+ snew_aligned(ic->tabq_coul_FDV0, ic->tabq_size*4, 32);
+ snew_aligned(ic->tabq_coul_F, ic->tabq_size, 32);
+ snew_aligned(ic->tabq_coul_V, ic->tabq_size, 32);
+ table_spline3_fill_ewald_lr(ic->tabq_coul_F, ic->tabq_coul_V, ic->tabq_coul_FDV0,
+ ic->tabq_size, 1/ic->tabq_scale, ic->ewaldcoeff_q, v_q_ewald_lr);
+ }
+
+ if (EVDW_PME(ic->vdwtype))
+ {
+ snew_aligned(ic->tabq_vdw_FDV0, ic->tabq_size*4, 32);
+ snew_aligned(ic->tabq_vdw_F, ic->tabq_size, 32);
+ snew_aligned(ic->tabq_vdw_V, ic->tabq_size, 32);
+ table_spline3_fill_ewald_lr(ic->tabq_vdw_F, ic->tabq_vdw_V, ic->tabq_vdw_FDV0,
+ ic->tabq_size, 1/ic->tabq_scale, ic->ewaldcoeff_lj, v_lj_ewald_lr);
+ }
+}
+
+void init_interaction_const_tables(FILE *fp,
+ interaction_const_t *ic,
+ gmx_bool bUsesSimpleTables,
+ real rtab)
+{
+ real spacing;
+
+ if (ic->eeltype == eelEWALD || EEL_PME(ic->eeltype) || EVDW_PME(ic->vdwtype))
+ {
+ init_ewald_f_table(ic, bUsesSimpleTables, rtab);
+
+ if (fp != NULL)
+ {
+ fprintf(fp, "Initialized non-bonded Ewald correction tables, spacing: %.2e size: %d\n\n",
+ 1/ic->tabq_scale, ic->tabq_size);
+ }
+ }
+}
+
+static void clear_force_switch_constants(shift_consts_t *sc)
+{
+ sc->c2 = 0;
+ sc->c3 = 0;
+ sc->cpot = 0;
+}
+
+static void force_switch_constants(real p,
+ real rsw, real rc,
+ shift_consts_t *sc)
+{
+ /* Here we determine the coefficient for shifting the force to zero
+ * between distance rsw and the cut-off rc.
+ * For a potential of r^-p, we have force p*r^-(p+1).
+ * But to save flops we absorb p in the coefficient.
+ * Thus we get:
+ * force/p = r^-(p+1) + c2*r^2 + c3*r^3
+ * potential = r^-p + c2/3*r^3 + c3/4*r^4 + cpot
+ */
+ sc->c2 = ((p + 1)*rsw - (p + 4)*rc)/(pow(rc, p + 2)*pow(rc - rsw, 2));
+ sc->c3 = -((p + 1)*rsw - (p + 3)*rc)/(pow(rc, p + 2)*pow(rc - rsw, 3));
+ sc->cpot = -pow(rc, -p) + p*sc->c2/3*pow(rc - rsw, 3) + p*sc->c3/4*pow(rc - rsw, 4);
+}
+
+static void potential_switch_constants(real rsw, real rc,
+ switch_consts_t *sc)
+{
+ /* The switch function is 1 at rsw and 0 at rc.
+ * The derivative and second derivate are zero at both ends.
+ * rsw = max(r - r_switch, 0)
+ * sw = 1 + c3*rsw^3 + c4*rsw^4 + c5*rsw^5
+ * dsw = 3*c3*rsw^2 + 4*c4*rsw^3 + 5*c5*rsw^4
+ * force = force*dsw - potential*sw
+ * potential *= sw
+ */
+ sc->c3 = -10*pow(rc - rsw, -3);
+ sc->c4 = 15*pow(rc - rsw, -4);
+ sc->c5 = -6*pow(rc - rsw, -5);
+}
+
+static void
+init_interaction_const(FILE *fp,
+ const t_commrec gmx_unused *cr,
+ interaction_const_t **interaction_const,
+ const t_forcerec *fr,
+ real rtab)
+{
+ interaction_const_t *ic;
+ gmx_bool bUsesSimpleTables = TRUE;
+
+ snew(ic, 1);
+
+ /* Just allocate something so we can free it */
+ snew_aligned(ic->tabq_coul_FDV0, 16, 32);
+ snew_aligned(ic->tabq_coul_F, 16, 32);
+ snew_aligned(ic->tabq_coul_V, 16, 32);
+
+ ic->rlist = fr->rlist;
+ ic->rlistlong = fr->rlistlong;
+
+ /* Lennard-Jones */
+ ic->vdwtype = fr->vdwtype;
+ ic->vdw_modifier = fr->vdw_modifier;
+ ic->rvdw = fr->rvdw;
+ ic->rvdw_switch = fr->rvdw_switch;
+ ic->ewaldcoeff_lj = fr->ewaldcoeff_lj;
+ ic->ljpme_comb_rule = fr->ljpme_combination_rule;
+ ic->sh_lj_ewald = 0;
+ clear_force_switch_constants(&ic->dispersion_shift);
+ clear_force_switch_constants(&ic->repulsion_shift);
+
+ switch (ic->vdw_modifier)
+ {
+ case eintmodPOTSHIFT:
+ /* Only shift the potential, don't touch the force */
+ ic->dispersion_shift.cpot = -pow(ic->rvdw, -6.0);
+ ic->repulsion_shift.cpot = -pow(ic->rvdw, -12.0);
+ if (EVDW_PME(ic->vdwtype))
+ {
+ real crc2;
+
+ crc2 = sqr(ic->ewaldcoeff_lj*ic->rvdw);
+ ic->sh_lj_ewald = (exp(-crc2)*(1 + crc2 + 0.5*crc2*crc2) - 1)*pow(ic->rvdw, -6.0);
+ }
+ break;
+ case eintmodFORCESWITCH:
+ /* Switch the force, switch and shift the potential */
+ force_switch_constants(6.0, ic->rvdw_switch, ic->rvdw,
+ &ic->dispersion_shift);
+ force_switch_constants(12.0, ic->rvdw_switch, ic->rvdw,
+ &ic->repulsion_shift);
+ break;
+ case eintmodPOTSWITCH:
+ /* Switch the potential and force */
+ potential_switch_constants(ic->rvdw_switch, ic->rvdw,
+ &ic->vdw_switch);
+ break;
+ case eintmodNONE:
+ case eintmodEXACTCUTOFF:
+ /* Nothing to do here */
+ break;
+ default:
+ gmx_incons("unimplemented potential modifier");
+ }
+
+ ic->sh_invrc6 = -ic->dispersion_shift.cpot;
+
+ /* Electrostatics */
+ ic->eeltype = fr->eeltype;
+ ic->coulomb_modifier = fr->coulomb_modifier;
+ ic->rcoulomb = fr->rcoulomb;
+ ic->epsilon_r = fr->epsilon_r;
+ ic->epsfac = fr->epsfac;
+ ic->ewaldcoeff_q = fr->ewaldcoeff_q;
+
+ if (fr->coulomb_modifier == eintmodPOTSHIFT)
+ {
+ ic->sh_ewald = gmx_erfc(ic->ewaldcoeff_q*ic->rcoulomb);
+ }
+ else
+ {
+ ic->sh_ewald = 0;
+ }
+
+ /* Reaction-field */
+ if (EEL_RF(ic->eeltype))
+ {
+ ic->epsilon_rf = fr->epsilon_rf;
+ ic->k_rf = fr->k_rf;
+ ic->c_rf = fr->c_rf;
+ }
+ else
+ {
+ /* For plain cut-off we might use the reaction-field kernels */
+ ic->epsilon_rf = ic->epsilon_r;
+ ic->k_rf = 0;
+ if (fr->coulomb_modifier == eintmodPOTSHIFT)
+ {
+ ic->c_rf = 1/ic->rcoulomb;
+ }
+ else
+ {
+ ic->c_rf = 0;
+ }
+ }
+
+ if (fp != NULL)
+ {
+ real dispersion_shift;
+
+ dispersion_shift = ic->dispersion_shift.cpot;
+ if (EVDW_PME(ic->vdwtype))
+ {
+ dispersion_shift -= ic->sh_lj_ewald;
+ }
+ fprintf(fp, "Potential shift: LJ r^-12: %.3e r^-6: %.3e",
+ ic->repulsion_shift.cpot, dispersion_shift);
+
+ if (ic->eeltype == eelCUT)
+ {
+ fprintf(fp, ", Coulomb %.e", -ic->c_rf);
+ }
+ else if (EEL_PME(ic->eeltype))
+ {
+ fprintf(fp, ", Ewald %.3e", -ic->sh_ewald);
+ }
+ fprintf(fp, "\n");
+ }
+
+ *interaction_const = ic;
+
+ if (fr->nbv != NULL && fr->nbv->bUseGPU)
+ {
+ nbnxn_cuda_init_const(fr->nbv->cu_nbv, ic, fr->nbv->grp);
+
+ /* With tMPI + GPUs some ranks may be sharing GPU(s) and therefore
+ * also sharing texture references. To keep the code simple, we don't
+ * treat texture references as shared resources, but this means that
+ * the coulomb_tab and nbfp texture refs will get updated by multiple threads.
+ * Hence, to ensure that the non-bonded kernels don't start before all
+ * texture binding operations are finished, we need to wait for all ranks
+ * to arrive here before continuing.
+ *
+ * Note that we could omit this barrier if GPUs are not shared (or
+ * texture objects are used), but as this is initialization code, there
+ * is not point in complicating things.
+ */
+#ifdef GMX_THREAD_MPI
+ if (PAR(cr))
+ {
+ gmx_barrier(cr);
+ }
+#endif /* GMX_THREAD_MPI */
+ }
+
+ bUsesSimpleTables = uses_simple_tables(fr->cutoff_scheme, fr->nbv, -1);
+ init_interaction_const_tables(fp, ic, bUsesSimpleTables, rtab);
+}
+
+static void init_nb_verlet(FILE *fp,
+ nonbonded_verlet_t **nb_verlet,
+ gmx_bool bFEP_NonBonded,
+ const t_inputrec *ir,
+ const t_forcerec *fr,
+ const t_commrec *cr,
+ const char *nbpu_opt)
+{
+ nonbonded_verlet_t *nbv;
+ int i;
+ char *env;
+ gmx_bool bEmulateGPU, bHybridGPURun = FALSE;
+
+ nbnxn_alloc_t *nb_alloc;
+ nbnxn_free_t *nb_free;
+
+ snew(nbv, 1);
+
+ pick_nbnxn_resources(cr, fr->hwinfo,
+ fr->bNonbonded,
+ &nbv->bUseGPU,
+ &bEmulateGPU,
+ fr->gpu_opt);
+
+ nbv->nbs = NULL;
+
+ nbv->ngrp = (DOMAINDECOMP(cr) ? 2 : 1);
+ for (i = 0; i < nbv->ngrp; i++)
+ {
+ nbv->grp[i].nbl_lists.nnbl = 0;
+ nbv->grp[i].nbat = NULL;
+ nbv->grp[i].kernel_type = nbnxnkNotSet;
+
+ if (i == 0) /* local */
+ {
+ pick_nbnxn_kernel(fp, cr, fr->use_simd_kernels,
+ nbv->bUseGPU, bEmulateGPU, ir,
+ &nbv->grp[i].kernel_type,
+ &nbv->grp[i].ewald_excl,
+ fr->bNonbonded);
+ }
+ else /* non-local */
+ {
+ if (nbpu_opt != NULL && strcmp(nbpu_opt, "gpu_cpu") == 0)
+ {
+ /* Use GPU for local, select a CPU kernel for non-local */
+ pick_nbnxn_kernel(fp, cr, fr->use_simd_kernels,
+ FALSE, FALSE, ir,
+ &nbv->grp[i].kernel_type,
+ &nbv->grp[i].ewald_excl,
+ fr->bNonbonded);
+
+ bHybridGPURun = TRUE;
+ }
+ else
+ {
+ /* Use the same kernel for local and non-local interactions */
+ nbv->grp[i].kernel_type = nbv->grp[0].kernel_type;
+ nbv->grp[i].ewald_excl = nbv->grp[0].ewald_excl;
+ }
+ }
+ }
+
+ if (nbv->bUseGPU)
+ {
+ /* init the NxN GPU data; the last argument tells whether we'll have
+ * both local and non-local NB calculation on GPU */
+ nbnxn_cuda_init(fp, &nbv->cu_nbv,
+ &fr->hwinfo->gpu_info, fr->gpu_opt,
+ cr->rank_pp_intranode,
+ (nbv->ngrp > 1) && !bHybridGPURun);
+
+ if ((env = getenv("GMX_NB_MIN_CI")) != NULL)
+ {
+ char *end;
+
+ nbv->min_ci_balanced = strtol(env, &end, 10);
+ if (!end || (*end != 0) || nbv->min_ci_balanced <= 0)
+ {
+ gmx_fatal(FARGS, "Invalid value passed in GMX_NB_MIN_CI=%s, positive integer required", env);
+ }
+
+ if (debug)
+ {
+ fprintf(debug, "Neighbor-list balancing parameter: %d (passed as env. var.)\n",
+ nbv->min_ci_balanced);
+ }
+ }
+ else
+ {
+ nbv->min_ci_balanced = nbnxn_cuda_min_ci_balanced(nbv->cu_nbv);
+ if (debug)
+ {
+ fprintf(debug, "Neighbor-list balancing parameter: %d (auto-adjusted to the number of GPU multi-processors)\n",
+ nbv->min_ci_balanced);
+ }
+ }
+ }
+ else
+ {
+ nbv->min_ci_balanced = 0;
+ }
+
+ *nb_verlet = nbv;
+
+ nbnxn_init_search(&nbv->nbs,
+ DOMAINDECOMP(cr) ? &cr->dd->nc : NULL,
+ DOMAINDECOMP(cr) ? domdec_zones(cr->dd) : NULL,
+ bFEP_NonBonded,
+ gmx_omp_nthreads_get(emntNonbonded));
+
+ for (i = 0; i < nbv->ngrp; i++)
+ {
+ if (nbv->grp[0].kernel_type == nbnxnk8x8x8_CUDA)
+ {
+ nb_alloc = &pmalloc;
+ nb_free = &pfree;
+ }
+ else
+ {
+ nb_alloc = NULL;
+ nb_free = NULL;
+ }
+
+ nbnxn_init_pairlist_set(&nbv->grp[i].nbl_lists,
+ nbnxn_kernel_pairlist_simple(nbv->grp[i].kernel_type),
+ /* 8x8x8 "non-simple" lists are ATM always combined */
+ !nbnxn_kernel_pairlist_simple(nbv->grp[i].kernel_type),
+ nb_alloc, nb_free);
+
+ if (i == 0 ||
+ nbv->grp[0].kernel_type != nbv->grp[i].kernel_type)
+ {
+ gmx_bool bSimpleList;
+ int enbnxninitcombrule;
+
+ bSimpleList = nbnxn_kernel_pairlist_simple(nbv->grp[i].kernel_type);
+
+ if (bSimpleList && (fr->vdwtype == evdwCUT && (fr->vdw_modifier == eintmodNONE || fr->vdw_modifier == eintmodPOTSHIFT)))
+ {
+ /* Plain LJ cut-off: we can optimize with combination rules */
+ enbnxninitcombrule = enbnxninitcombruleDETECT;
+ }
+ else if (fr->vdwtype == evdwPME)
+ {
+ /* LJ-PME: we need to use a combination rule for the grid */
+ if (fr->ljpme_combination_rule == eljpmeGEOM)
+ {
+ enbnxninitcombrule = enbnxninitcombruleGEOM;
+ }
+ else
+ {
+ enbnxninitcombrule = enbnxninitcombruleLB;
+ }
+ }
+ else
+ {
+ /* We use a full combination matrix: no rule required */
+ enbnxninitcombrule = enbnxninitcombruleNONE;
+ }
+
+
+ snew(nbv->grp[i].nbat, 1);
+ nbnxn_atomdata_init(fp,
+ nbv->grp[i].nbat,
+ nbv->grp[i].kernel_type,
+ enbnxninitcombrule,
+ fr->ntype, fr->nbfp,
+ ir->opts.ngener,
+ bSimpleList ? gmx_omp_nthreads_get(emntNonbonded) : 1,
+ nb_alloc, nb_free);
+ }
+ else
+ {
+ nbv->grp[i].nbat = nbv->grp[0].nbat;
+ }
+ }
+}
+
+void init_forcerec(FILE *fp,
+ const output_env_t oenv,
+ t_forcerec *fr,
+ t_fcdata *fcd,
+ const t_inputrec *ir,
+ const gmx_mtop_t *mtop,
+ const t_commrec *cr,
+ matrix box,
+ const char *tabfn,
+ const char *tabafn,
+ const char *tabpfn,
+ const char *tabbfn,
+ const char *nbpu_opt,
+ gmx_bool bNoSolvOpt,
+ real print_force)
+{
+ int i, j, m, natoms, ngrp, negp_pp, negptable, egi, egj;
+ real rtab;
+ char *env;
+ double dbl;
+ const t_block *cgs;
+ gmx_bool bGenericKernelOnly;
+ gmx_bool bMakeTables, bMakeSeparate14Table, bSomeNormalNbListsAreInUse;
+ gmx_bool bFEP_NonBonded;
+ t_nblists *nbl;
+ int *nm_ind, egp_flags;
+
+ if (fr->hwinfo == NULL)
+ {
+ /* Detect hardware, gather information.
+ * In mdrun, hwinfo has already been set before calling init_forcerec.
+ * Here we ignore GPUs, as tools will not use them anyhow.
+ */
+ fr->hwinfo = gmx_detect_hardware(fp, cr, FALSE);
+ }
+
+ /* By default we turn SIMD kernels on, but it might be turned off further down... */
+ fr->use_simd_kernels = TRUE;
+
+ fr->bDomDec = DOMAINDECOMP(cr);
+
+ natoms = mtop->natoms;
+
+ if (check_box(ir->ePBC, box))
+ {
+ gmx_fatal(FARGS, check_box(ir->ePBC, box));
+ }
+
+ /* Test particle insertion ? */
+ if (EI_TPI(ir->eI))
+ {
+ /* Set to the size of the molecule to be inserted (the last one) */
+ /* Because of old style topologies, we have to use the last cg
+ * instead of the last molecule type.
+ */
+ cgs = &mtop->moltype[mtop->molblock[mtop->nmolblock-1].type].cgs;
+ fr->n_tpi = cgs->index[cgs->nr] - cgs->index[cgs->nr-1];
+ if (fr->n_tpi != mtop->mols.index[mtop->mols.nr] - mtop->mols.index[mtop->mols.nr-1])
+ {
+ gmx_fatal(FARGS, "The molecule to insert can not consist of multiple charge groups.\nMake it a single charge group.");
+ }
+ }
+ else
+ {
+ fr->n_tpi = 0;
+ }
+
+ /* Copy AdResS parameters */
+ if (ir->bAdress)
+ {
+ fr->adress_type = ir->adress->type;
+ fr->adress_const_wf = ir->adress->const_wf;
+ fr->adress_ex_width = ir->adress->ex_width;
+ fr->adress_hy_width = ir->adress->hy_width;
+ fr->adress_icor = ir->adress->icor;
+ fr->adress_site = ir->adress->site;
+ fr->adress_ex_forcecap = ir->adress->ex_forcecap;
+ fr->adress_do_hybridpairs = ir->adress->do_hybridpairs;
+
+
+ snew(fr->adress_group_explicit, ir->adress->n_energy_grps);
+ for (i = 0; i < ir->adress->n_energy_grps; i++)
+ {
+ fr->adress_group_explicit[i] = ir->adress->group_explicit[i];
+ }
+
+ fr->n_adress_tf_grps = ir->adress->n_tf_grps;
+ snew(fr->adress_tf_table_index, fr->n_adress_tf_grps);
+ for (i = 0; i < fr->n_adress_tf_grps; i++)
+ {
+ fr->adress_tf_table_index[i] = ir->adress->tf_table_index[i];
+ }
+ copy_rvec(ir->adress->refs, fr->adress_refs);
+ }
+ else
+ {
+ fr->adress_type = eAdressOff;
+ fr->adress_do_hybridpairs = FALSE;
+ }
+
+ /* Copy the user determined parameters */
+ fr->userint1 = ir->userint1;
+ fr->userint2 = ir->userint2;
+ fr->userint3 = ir->userint3;
+ fr->userint4 = ir->userint4;
+ fr->userreal1 = ir->userreal1;
+ fr->userreal2 = ir->userreal2;
+ fr->userreal3 = ir->userreal3;
+ fr->userreal4 = ir->userreal4;
+
+ /* Shell stuff */
+ fr->fc_stepsize = ir->fc_stepsize;
+
+ /* Free energy */
+ fr->efep = ir->efep;
+ fr->sc_alphavdw = ir->fepvals->sc_alpha;
+ if (ir->fepvals->bScCoul)
+ {
+ fr->sc_alphacoul = ir->fepvals->sc_alpha;
+ fr->sc_sigma6_min = pow(ir->fepvals->sc_sigma_min, 6);
+ }
+ else
+ {
+ fr->sc_alphacoul = 0;
+ fr->sc_sigma6_min = 0; /* only needed when bScCoul is on */
+ }
+ fr->sc_power = ir->fepvals->sc_power;
+ fr->sc_r_power = ir->fepvals->sc_r_power;
+ fr->sc_sigma6_def = pow(ir->fepvals->sc_sigma, 6);
+
+ env = getenv("GMX_SCSIGMA_MIN");
+ if (env != NULL)
+ {
+ dbl = 0;
+ sscanf(env, "%lf", &dbl);
+ fr->sc_sigma6_min = pow(dbl, 6);
+ if (fp)
+ {
+ fprintf(fp, "Setting the minimum soft core sigma to %g nm\n", dbl);
+ }
+ }
+
+ fr->bNonbonded = TRUE;
+ if (getenv("GMX_NO_NONBONDED") != NULL)
+ {
+ /* turn off non-bonded calculations */
+ fr->bNonbonded = FALSE;
+ md_print_warn(cr, fp,
+ "Found environment variable GMX_NO_NONBONDED.\n"
+ "Disabling nonbonded calculations.\n");
+ }
+
+ bGenericKernelOnly = FALSE;
+
+ /* We now check in the NS code whether a particular combination of interactions
+ * can be used with water optimization, and disable it if that is not the case.
+ */
+
+ if (getenv("GMX_NB_GENERIC") != NULL)
+ {
+ if (fp != NULL)
+ {
+ fprintf(fp,
+ "Found environment variable GMX_NB_GENERIC.\n"
+ "Disabling all interaction-specific nonbonded kernels, will only\n"
+ "use the slow generic ones in src/gmxlib/nonbonded/nb_generic.c\n\n");
+ }
+ bGenericKernelOnly = TRUE;
+ }
+
+ if (bGenericKernelOnly == TRUE)
+ {
+ bNoSolvOpt = TRUE;
+ }
+
+ if ( (getenv("GMX_DISABLE_SIMD_KERNELS") != NULL) || (getenv("GMX_NOOPTIMIZEDKERNELS") != NULL) )
+ {
+ fr->use_simd_kernels = FALSE;
+ if (fp != NULL)
+ {
+ fprintf(fp,
+ "\nFound environment variable GMX_DISABLE_SIMD_KERNELS.\n"
+ "Disabling the usage of any SIMD-specific kernel routines (e.g. SSE2/SSE4.1/AVX).\n\n");
+ }
+ }
+
+ fr->bBHAM = (mtop->ffparams.functype[0] == F_BHAM);
+
+ /* Check if we can/should do all-vs-all kernels */
+ fr->bAllvsAll = can_use_allvsall(ir, FALSE, NULL, NULL);
+ fr->AllvsAll_work = NULL;
+ fr->AllvsAll_workgb = NULL;
+
+ /* All-vs-all kernels have not been implemented in 4.6, and
+ * the SIMD group kernels are also buggy in this case. Non-SIMD
+ * group kernels are OK. See Redmine #1249. */
+ if (fr->bAllvsAll)
+ {
+ fr->bAllvsAll = FALSE;
+ fr->use_simd_kernels = FALSE;
+ if (fp != NULL)
+ {
+ fprintf(fp,
+ "\nYour simulation settings would have triggered the efficient all-vs-all\n"
+ "kernels in GROMACS 4.5, but these have not been implemented in GROMACS\n"
+ "4.6. Also, we can't use the accelerated SIMD kernels here because\n"
+ "of an unfixed bug. The reference C kernels are correct, though, so\n"
+ "we are proceeding by disabling all CPU architecture-specific\n"
+ "(e.g. SSE2/SSE4/AVX) routines. If performance is important, please\n"
+ "use GROMACS 4.5.7 or try cutoff-scheme = Verlet.\n\n");
+ }
+ }
+
+ /* Neighbour searching stuff */
+ fr->cutoff_scheme = ir->cutoff_scheme;
+ fr->bGrid = (ir->ns_type == ensGRID);
+ fr->ePBC = ir->ePBC;
+
+ if (fr->cutoff_scheme == ecutsGROUP)
+ {
+ const char *note = "NOTE: This file uses the deprecated 'group' cutoff_scheme. This will be\n"
+ "removed in a future release when 'verlet' supports all interaction forms.\n";
+
+ if (MASTER(cr))
+ {
+ fprintf(stderr, "\n%s\n", note);
+ }
+ if (fp != NULL)
+ {
+ fprintf(fp, "\n%s\n", note);
+ }
+ }
+
+ /* Determine if we will do PBC for distances in bonded interactions */
+ if (fr->ePBC == epbcNONE)
+ {
+ fr->bMolPBC = FALSE;
+ }
+ else
+ {
+ if (!DOMAINDECOMP(cr))
+ {
+ /* The group cut-off scheme and SHAKE assume charge groups
+ * are whole, but not using molpbc is faster in most cases.
+ */
+ if (fr->cutoff_scheme == ecutsGROUP ||
+ (ir->eConstrAlg == econtSHAKE &&
+ (gmx_mtop_ftype_count(mtop, F_CONSTR) > 0 ||
+ gmx_mtop_ftype_count(mtop, F_CONSTRNC) > 0)))
+ {
+ fr->bMolPBC = ir->bPeriodicMols;
+ }
+ else
+ {
+ fr->bMolPBC = TRUE;
+ if (getenv("GMX_USE_GRAPH") != NULL)
+ {
+ fr->bMolPBC = FALSE;
+ if (fp)
+ {
+ fprintf(fp, "\nGMX_MOLPBC is set, using the graph for bonded interactions\n\n");
+ }
+ }
+ }
+ }
+ else
+ {
+ fr->bMolPBC = dd_bonded_molpbc(cr->dd, fr->ePBC);
+ }
+ }
+ fr->bGB = (ir->implicit_solvent == eisGBSA);
+
+ fr->rc_scaling = ir->refcoord_scaling;
+ copy_rvec(ir->posres_com, fr->posres_com);
+ copy_rvec(ir->posres_comB, fr->posres_comB);
+ fr->rlist = cutoff_inf(ir->rlist);
+ fr->rlistlong = cutoff_inf(ir->rlistlong);
+ fr->eeltype = ir->coulombtype;
+ fr->vdwtype = ir->vdwtype;
+ fr->ljpme_combination_rule = ir->ljpme_combination_rule;
+
+ fr->coulomb_modifier = ir->coulomb_modifier;
+ fr->vdw_modifier = ir->vdw_modifier;
+
+ /* Electrostatics: Translate from interaction-setting-in-mdp-file to kernel interaction format */
+ switch (fr->eeltype)
+ {
+ case eelCUT:
+ fr->nbkernel_elec_interaction = (fr->bGB) ? GMX_NBKERNEL_ELEC_GENERALIZEDBORN : GMX_NBKERNEL_ELEC_COULOMB;
+ break;
+
+ case eelRF:
+ case eelGRF:
+ case eelRF_NEC:
+ fr->nbkernel_elec_interaction = GMX_NBKERNEL_ELEC_REACTIONFIELD;
+ break;
+
+ case eelRF_ZERO:
+ fr->nbkernel_elec_interaction = GMX_NBKERNEL_ELEC_REACTIONFIELD;
+ fr->coulomb_modifier = eintmodEXACTCUTOFF;
+ break;
+
+ case eelSWITCH:
+ case eelSHIFT:
+ case eelUSER:
+ case eelENCADSHIFT:
+ case eelPMESWITCH:
+ case eelPMEUSER:
+ case eelPMEUSERSWITCH:
+ fr->nbkernel_elec_interaction = GMX_NBKERNEL_ELEC_CUBICSPLINETABLE;
+ break;
+
+ case eelPME:
+ case eelEWALD:
+ fr->nbkernel_elec_interaction = GMX_NBKERNEL_ELEC_EWALD;
+ break;
+
+ default:
+ gmx_fatal(FARGS, "Unsupported electrostatic interaction: %s", eel_names[fr->eeltype]);
+ break;
+ }
+
+ /* Vdw: Translate from mdp settings to kernel format */
+ switch (fr->vdwtype)
+ {
+ case evdwCUT:
+ if (fr->bBHAM)
+ {
+ fr->nbkernel_vdw_interaction = GMX_NBKERNEL_VDW_BUCKINGHAM;
+ }
+ else
+ {
+ fr->nbkernel_vdw_interaction = GMX_NBKERNEL_VDW_LENNARDJONES;
+ }
+ break;
+ case evdwPME:
+ fr->nbkernel_vdw_interaction = GMX_NBKERNEL_VDW_LJEWALD;
+ break;
+
+ case evdwSWITCH:
+ case evdwSHIFT:
+ case evdwUSER:
+ case evdwENCADSHIFT:
+ fr->nbkernel_vdw_interaction = GMX_NBKERNEL_VDW_CUBICSPLINETABLE;
+ break;
+
+ default:
+ gmx_fatal(FARGS, "Unsupported vdw interaction: %s", evdw_names[fr->vdwtype]);
+ break;
+ }
+
+ /* These start out identical to ir, but might be altered if we e.g. tabulate the interaction in the kernel */
+ fr->nbkernel_elec_modifier = fr->coulomb_modifier;
+ fr->nbkernel_vdw_modifier = fr->vdw_modifier;
+
+ fr->bTwinRange = fr->rlistlong > fr->rlist;
+ fr->bEwald = (EEL_PME(fr->eeltype) || fr->eeltype == eelEWALD);
+
+ fr->reppow = mtop->ffparams.reppow;
+
+ if (ir->cutoff_scheme == ecutsGROUP)
+ {
+ fr->bvdwtab = ((fr->vdwtype != evdwCUT || !gmx_within_tol(fr->reppow, 12.0, 10*GMX_DOUBLE_EPS))
+ && !EVDW_PME(fr->vdwtype));
+ /* We have special kernels for standard Ewald and PME, but the pme-switch ones are tabulated above */
+ fr->bcoultab = !(fr->eeltype == eelCUT ||
+ fr->eeltype == eelEWALD ||
+ fr->eeltype == eelPME ||
+ fr->eeltype == eelRF ||
+ fr->eeltype == eelRF_ZERO);
+
+ /* If the user absolutely wants different switch/shift settings for coul/vdw, it is likely
+ * going to be faster to tabulate the interaction than calling the generic kernel.
+ */
+ if (fr->nbkernel_elec_modifier == eintmodPOTSWITCH && fr->nbkernel_vdw_modifier == eintmodPOTSWITCH)
+ {
+ if ((fr->rcoulomb_switch != fr->rvdw_switch) || (fr->rcoulomb != fr->rvdw))
+ {
+ fr->bcoultab = TRUE;
+ }
+ }
+ else if ((fr->nbkernel_elec_modifier == eintmodPOTSHIFT && fr->nbkernel_vdw_modifier == eintmodPOTSHIFT) ||
+ ((fr->nbkernel_elec_interaction == GMX_NBKERNEL_ELEC_REACTIONFIELD &&
+ fr->nbkernel_elec_modifier == eintmodEXACTCUTOFF &&
+ (fr->nbkernel_vdw_modifier == eintmodPOTSWITCH || fr->nbkernel_vdw_modifier == eintmodPOTSHIFT))))
+ {
+ if (fr->rcoulomb != fr->rvdw)
+ {
+ fr->bcoultab = TRUE;
+ }
+ }
+
+ if (getenv("GMX_REQUIRE_TABLES"))
+ {
+ fr->bvdwtab = TRUE;
+ fr->bcoultab = TRUE;
+ }
+
+ if (fp)
+ {
+ fprintf(fp, "Table routines are used for coulomb: %s\n", bool_names[fr->bcoultab]);
+ fprintf(fp, "Table routines are used for vdw: %s\n", bool_names[fr->bvdwtab ]);
+ }
+
+ if (fr->bvdwtab == TRUE)
+ {
+ fr->nbkernel_vdw_interaction = GMX_NBKERNEL_VDW_CUBICSPLINETABLE;
+ fr->nbkernel_vdw_modifier = eintmodNONE;
+ }
+ if (fr->bcoultab == TRUE)
+ {
+ fr->nbkernel_elec_interaction = GMX_NBKERNEL_ELEC_CUBICSPLINETABLE;
+ fr->nbkernel_elec_modifier = eintmodNONE;
+ }
+ }
+
+ if (ir->cutoff_scheme == ecutsVERLET)
+ {
+ if (!gmx_within_tol(fr->reppow, 12.0, 10*GMX_DOUBLE_EPS))
+ {
+ gmx_fatal(FARGS, "Cut-off scheme %S only supports LJ repulsion power 12", ecutscheme_names[ir->cutoff_scheme]);
+ }
+ fr->bvdwtab = FALSE;
+ fr->bcoultab = FALSE;
+ }
+
+ /* Tables are used for direct ewald sum */
+ if (fr->bEwald)
+ {
+ if (EEL_PME(ir->coulombtype))
+ {
+ if (fp)
+ {
+ fprintf(fp, "Will do PME sum in reciprocal space for electrostatic interactions.\n");
+ }
+ if (ir->coulombtype == eelP3M_AD)
+ {
+ please_cite(fp, "Hockney1988");
+ please_cite(fp, "Ballenegger2012");
+ }
+ else
+ {
+ please_cite(fp, "Essmann95a");
+ }
+
+ if (ir->ewald_geometry == eewg3DC)
+ {
+ if (fp)
+ {
+ fprintf(fp, "Using the Ewald3DC correction for systems with a slab geometry.\n");
+ }
+ please_cite(fp, "In-Chul99a");
+ }
+ }
+ fr->ewaldcoeff_q = calc_ewaldcoeff_q(ir->rcoulomb, ir->ewald_rtol);
+ init_ewald_tab(&(fr->ewald_table), ir, fp);
+ if (fp)
+ {
+ fprintf(fp, "Using a Gaussian width (1/beta) of %g nm for Ewald\n",
+ 1/fr->ewaldcoeff_q);
+ }
+ }
+
+ if (EVDW_PME(ir->vdwtype))
+ {
+ if (fp)
+ {
+ fprintf(fp, "Will do PME sum in reciprocal space for LJ dispersion interactions.\n");
+ }
+ please_cite(fp, "Essmann95a");
+ fr->ewaldcoeff_lj = calc_ewaldcoeff_lj(ir->rvdw, ir->ewald_rtol_lj);
+ if (fp)
+ {
+ fprintf(fp, "Using a Gaussian width (1/beta) of %g nm for LJ Ewald\n",
+ 1/fr->ewaldcoeff_lj);
+ }
+ }
+
+ /* Electrostatics */
+ fr->epsilon_r = ir->epsilon_r;
+ fr->epsilon_rf = ir->epsilon_rf;
+ fr->fudgeQQ = mtop->ffparams.fudgeQQ;
+ fr->rcoulomb_switch = ir->rcoulomb_switch;
+ fr->rcoulomb = cutoff_inf(ir->rcoulomb);
+
+ /* Parameters for generalized RF */
+ fr->zsquare = 0.0;
+ fr->temp = 0.0;
+
+ if (fr->eeltype == eelGRF)
+ {
+ init_generalized_rf(fp, mtop, ir, fr);
+ }
+
+ fr->bF_NoVirSum = (EEL_FULL(fr->eeltype) || EVDW_PME(fr->vdwtype) ||
+ gmx_mtop_ftype_count(mtop, F_POSRES) > 0 ||
+ gmx_mtop_ftype_count(mtop, F_FBPOSRES) > 0 ||
+ IR_ELEC_FIELD(*ir) ||
+ (fr->adress_icor != eAdressICOff)
+ );
+
+ if (fr->cutoff_scheme == ecutsGROUP &&
+ ncg_mtop(mtop) > fr->cg_nalloc && !DOMAINDECOMP(cr))
+ {
+ /* Count the total number of charge groups */
+ fr->cg_nalloc = ncg_mtop(mtop);
+ srenew(fr->cg_cm, fr->cg_nalloc);
+ }
+ if (fr->shift_vec == NULL)
+ {
+ snew(fr->shift_vec, SHIFTS);
+ }
+
+ if (fr->fshift == NULL)
+ {
+ snew(fr->fshift, SHIFTS);
+ }
+
+ if (fr->nbfp == NULL)
+ {
+ fr->ntype = mtop->ffparams.atnr;
+ fr->nbfp = mk_nbfp(&mtop->ffparams, fr->bBHAM);
+ if (EVDW_PME(fr->vdwtype))
+ {
+ fr->ljpme_c6grid = make_ljpme_c6grid(&mtop->ffparams, fr);
+ }
+ }
+
+ /* Copy the energy group exclusions */
+ fr->egp_flags = ir->opts.egp_flags;
+
+ /* Van der Waals stuff */
+ fr->rvdw = cutoff_inf(ir->rvdw);
+ fr->rvdw_switch = ir->rvdw_switch;
+ if ((fr->vdwtype != evdwCUT) && (fr->vdwtype != evdwUSER) && !fr->bBHAM)
+ {
+ if (fr->rvdw_switch >= fr->rvdw)
+ {
+ gmx_fatal(FARGS, "rvdw_switch (%f) must be < rvdw (%f)",
+ fr->rvdw_switch, fr->rvdw);
+ }
+ if (fp)
+ {
+ fprintf(fp, "Using %s Lennard-Jones, switch between %g and %g nm\n",
+ (fr->eeltype == eelSWITCH) ? "switched" : "shifted",
+ fr->rvdw_switch, fr->rvdw);
+ }
+ }
+
+ if (fr->bBHAM && EVDW_PME(fr->vdwtype))
+ {
+ gmx_fatal(FARGS, "LJ PME not supported with Buckingham");
+ }
+
+ if (fr->bBHAM && (fr->vdwtype == evdwSHIFT || fr->vdwtype == evdwSWITCH))
+ {
+ gmx_fatal(FARGS, "Switch/shift interaction not supported with Buckingham");
++ }
++
++ if (fr->bBHAM && fr->cutoff_scheme == ecutsVERLET)
++ {
++ gmx_fatal(FARGS, "Verlet cutoff-scheme is not supported with Buckingham");
+ }
+
+ if (fp)
+ {
+ fprintf(fp, "Cut-off's: NS: %g Coulomb: %g %s: %g\n",
+ fr->rlist, fr->rcoulomb, fr->bBHAM ? "BHAM" : "LJ", fr->rvdw);
+ }
+
+ fr->eDispCorr = ir->eDispCorr;
+ if (ir->eDispCorr != edispcNO)
+ {
+ set_avcsixtwelve(fp, fr, mtop);
+ }
+
+ if (fr->bBHAM)
+ {
+ set_bham_b_max(fp, fr, mtop);
+ }
+
+ fr->gb_epsilon_solvent = ir->gb_epsilon_solvent;
+
+ /* Copy the GBSA data (radius, volume and surftens for each
+ * atomtype) from the topology atomtype section to forcerec.
+ */
+ snew(fr->atype_radius, fr->ntype);
+ snew(fr->atype_vol, fr->ntype);
+ snew(fr->atype_surftens, fr->ntype);
+ snew(fr->atype_gb_radius, fr->ntype);
+ snew(fr->atype_S_hct, fr->ntype);
+
+ if (mtop->atomtypes.nr > 0)
+ {
+ for (i = 0; i < fr->ntype; i++)
+ {
+ fr->atype_radius[i] = mtop->atomtypes.radius[i];
+ }
+ for (i = 0; i < fr->ntype; i++)
+ {
+ fr->atype_vol[i] = mtop->atomtypes.vol[i];
+ }
+ for (i = 0; i < fr->ntype; i++)
+ {
+ fr->atype_surftens[i] = mtop->atomtypes.surftens[i];
+ }
+ for (i = 0; i < fr->ntype; i++)
+ {
+ fr->atype_gb_radius[i] = mtop->atomtypes.gb_radius[i];
+ }
+ for (i = 0; i < fr->ntype; i++)
+ {
+ fr->atype_S_hct[i] = mtop->atomtypes.S_hct[i];
+ }
+ }
+
+ /* Generate the GB table if needed */
+ if (fr->bGB)
+ {
+#ifdef GMX_DOUBLE
+ fr->gbtabscale = 2000;
+#else
+ fr->gbtabscale = 500;
+#endif
+
+ fr->gbtabr = 100;
+ fr->gbtab = make_gb_table(oenv, fr);
+
+ init_gb(&fr->born, fr, ir, mtop, ir->gb_algorithm);
+
+ /* Copy local gb data (for dd, this is done in dd_partition_system) */
+ if (!DOMAINDECOMP(cr))
+ {
+ make_local_gb(cr, fr->born, ir->gb_algorithm);
+ }
+ }
+
+ /* Set the charge scaling */
+ if (fr->epsilon_r != 0)
+ {
+ fr->epsfac = ONE_4PI_EPS0/fr->epsilon_r;
+ }
+ else
+ {
+ /* eps = 0 is infinite dieletric: no coulomb interactions */
+ fr->epsfac = 0;
+ }
+
+ /* Reaction field constants */
+ if (EEL_RF(fr->eeltype))
+ {
+ calc_rffac(fp, fr->eeltype, fr->epsilon_r, fr->epsilon_rf,
+ fr->rcoulomb, fr->temp, fr->zsquare, box,
+ &fr->kappa, &fr->k_rf, &fr->c_rf);
+ }
+
+ /*This now calculates sum for q and c6*/
+ set_chargesum(fp, fr, mtop);
+
+ /* if we are using LR electrostatics, and they are tabulated,
+ * the tables will contain modified coulomb interactions.
+ * Since we want to use the non-shifted ones for 1-4
+ * coulombic interactions, we must have an extra set of tables.
+ */
+
+ /* Construct tables.
+ * A little unnecessary to make both vdw and coul tables sometimes,
+ * but what the heck... */
+
+ bMakeTables = fr->bcoultab || fr->bvdwtab || fr->bEwald ||
+ (ir->eDispCorr != edispcNO && ir_vdw_switched(ir));
+
+ bMakeSeparate14Table = ((!bMakeTables || fr->eeltype != eelCUT || fr->vdwtype != evdwCUT ||
+ fr->bBHAM || fr->bEwald) &&
+ (gmx_mtop_ftype_count(mtop, F_LJ14) > 0 ||
+ gmx_mtop_ftype_count(mtop, F_LJC14_Q) > 0 ||
+ gmx_mtop_ftype_count(mtop, F_LJC_PAIRS_NB) > 0));
+
+ negp_pp = ir->opts.ngener - ir->nwall;
+ negptable = 0;
+ if (!bMakeTables)
+ {
+ bSomeNormalNbListsAreInUse = TRUE;
+ fr->nnblists = 1;
+ }
+ else
+ {
+ bSomeNormalNbListsAreInUse = (ir->eDispCorr != edispcNO);
+ for (egi = 0; egi < negp_pp; egi++)
+ {
+ for (egj = egi; egj < negp_pp; egj++)
+ {
+ egp_flags = ir->opts.egp_flags[GID(egi, egj, ir->opts.ngener)];
+ if (!(egp_flags & EGP_EXCL))
+ {
+ if (egp_flags & EGP_TABLE)
+ {
+ negptable++;
+ }
+ else
+ {
+ bSomeNormalNbListsAreInUse = TRUE;
+ }
+ }
+ }
+ }
+ if (bSomeNormalNbListsAreInUse)
+ {
+ fr->nnblists = negptable + 1;
+ }
+ else
+ {
+ fr->nnblists = negptable;
+ }
+ if (fr->nnblists > 1)
+ {
+ snew(fr->gid2nblists, ir->opts.ngener*ir->opts.ngener);
+ }
+ }
+
+ if (ir->adress)
+ {
+ fr->nnblists *= 2;
+ }
+
+ snew(fr->nblists, fr->nnblists);
+
+ /* This code automatically gives table length tabext without cut-off's,
+ * in that case grompp should already have checked that we do not need
+ * normal tables and we only generate tables for 1-4 interactions.
+ */
+ rtab = ir->rlistlong + ir->tabext;
+
+ if (bMakeTables)
+ {
+ /* make tables for ordinary interactions */
+ if (bSomeNormalNbListsAreInUse)
+ {
+ make_nbf_tables(fp, oenv, fr, rtab, cr, tabfn, NULL, NULL, &fr->nblists[0]);
+ if (ir->adress)
+ {
+ make_nbf_tables(fp, oenv, fr, rtab, cr, tabfn, NULL, NULL, &fr->nblists[fr->nnblists/2]);
+ }
+ if (!bMakeSeparate14Table)
+ {
+ fr->tab14 = fr->nblists[0].table_elec_vdw;
+ }
+ m = 1;
+ }
+ else
+ {
+ m = 0;
+ }
+ if (negptable > 0)
+ {
+ /* Read the special tables for certain energy group pairs */
+ nm_ind = mtop->groups.grps[egcENER].nm_ind;
+ for (egi = 0; egi < negp_pp; egi++)
+ {
+ for (egj = egi; egj < negp_pp; egj++)
+ {
+ egp_flags = ir->opts.egp_flags[GID(egi, egj, ir->opts.ngener)];
+ if ((egp_flags & EGP_TABLE) && !(egp_flags & EGP_EXCL))
+ {
+ nbl = &(fr->nblists[m]);
+ if (fr->nnblists > 1)
+ {
+ fr->gid2nblists[GID(egi, egj, ir->opts.ngener)] = m;
+ }
+ /* Read the table file with the two energy groups names appended */
+ make_nbf_tables(fp, oenv, fr, rtab, cr, tabfn,
+ *mtop->groups.grpname[nm_ind[egi]],
+ *mtop->groups.grpname[nm_ind[egj]],
+ &fr->nblists[m]);
+ if (ir->adress)
+ {
+ make_nbf_tables(fp, oenv, fr, rtab, cr, tabfn,
+ *mtop->groups.grpname[nm_ind[egi]],
+ *mtop->groups.grpname[nm_ind[egj]],
+ &fr->nblists[fr->nnblists/2+m]);
+ }
+ m++;
+ }
+ else if (fr->nnblists > 1)
+ {
+ fr->gid2nblists[GID(egi, egj, ir->opts.ngener)] = 0;
+ }
+ }
+ }
+ }
+ }
+ if (bMakeSeparate14Table)
+ {
+ /* generate extra tables with plain Coulomb for 1-4 interactions only */
+ fr->tab14 = make_tables(fp, oenv, fr, MASTER(cr), tabpfn, rtab,
+ GMX_MAKETABLES_14ONLY);
+ }
+
+ /* Read AdResS Thermo Force table if needed */
+ if (fr->adress_icor == eAdressICThermoForce)
+ {
+ /* old todo replace */
+
+ if (ir->adress->n_tf_grps > 0)
+ {
+ make_adress_tf_tables(fp, oenv, fr, ir, tabfn, mtop, box);
+
+ }
+ else
+ {
+ /* load the default table */
+ snew(fr->atf_tabs, 1);
+ fr->atf_tabs[DEFAULT_TF_TABLE] = make_atf_table(fp, oenv, fr, tabafn, box);
+ }
+ }
+
+ /* Wall stuff */
+ fr->nwall = ir->nwall;
+ if (ir->nwall && ir->wall_type == ewtTABLE)
+ {
+ make_wall_tables(fp, oenv, ir, tabfn, &mtop->groups, fr);
+ }
+
+ if (fcd && tabbfn)
+ {
+ fcd->bondtab = make_bonded_tables(fp,
+ F_TABBONDS, F_TABBONDSNC,
+ mtop, tabbfn, "b");
+ fcd->angletab = make_bonded_tables(fp,
+ F_TABANGLES, -1,
+ mtop, tabbfn, "a");
+ fcd->dihtab = make_bonded_tables(fp,
+ F_TABDIHS, -1,
+ mtop, tabbfn, "d");
+ }
+ else
+ {
+ if (debug)
+ {
+ fprintf(debug, "No fcdata or table file name passed, can not read table, can not do bonded interactions\n");
+ }
+ }
+
+ /* QM/MM initialization if requested
+ */
+ if (ir->bQMMM)
+ {
+ fprintf(stderr, "QM/MM calculation requested.\n");
+ }
+
+ fr->bQMMM = ir->bQMMM;
+ fr->qr = mk_QMMMrec();
+
+ /* Set all the static charge group info */
+ fr->cginfo_mb = init_cginfo_mb(fp, mtop, fr, bNoSolvOpt,
+ &bFEP_NonBonded,
+ &fr->bExcl_IntraCGAll_InterCGNone);
+ if (DOMAINDECOMP(cr))
+ {
+ fr->cginfo = NULL;
+ }
+ else
+ {
+ fr->cginfo = cginfo_expand(mtop->nmolblock, fr->cginfo_mb);
+ }
+
+ if (!DOMAINDECOMP(cr))
+ {
+ forcerec_set_ranges(fr, ncg_mtop(mtop), ncg_mtop(mtop),
+ mtop->natoms, mtop->natoms, mtop->natoms);
+ }
+
+ fr->print_force = print_force;
+
+
+ /* coarse load balancing vars */
+ fr->t_fnbf = 0.;
+ fr->t_wait = 0.;
+ fr->timesteps = 0;
+
+ /* Initialize neighbor search */
+ init_ns(fp, cr, &fr->ns, fr, mtop);
+
+ if (cr->duty & DUTY_PP)
+ {
+ gmx_nonbonded_setup(fr, bGenericKernelOnly);
+ /*
+ if (ir->bAdress)
+ {
+ gmx_setup_adress_kernels(fp,bGenericKernelOnly);
+ }
+ */
+ }
+
+ /* Initialize the thread working data for bonded interactions */
+ init_forcerec_f_threads(fr, mtop->groups.grps[egcENER].nr);
+
+ snew(fr->excl_load, fr->nthreads+1);
+
+ if (fr->cutoff_scheme == ecutsVERLET)
+ {
+ if (ir->rcoulomb != ir->rvdw)
+ {
+ gmx_fatal(FARGS, "With Verlet lists rcoulomb and rvdw should be identical");
+ }
+
+ init_nb_verlet(fp, &fr->nbv, bFEP_NonBonded, ir, fr, cr, nbpu_opt);
+ }
+
+ /* fr->ic is used both by verlet and group kernels (to some extent) now */
+ init_interaction_const(fp, cr, &fr->ic, fr, rtab);
+
+ if (ir->eDispCorr != edispcNO)
+ {
+ calc_enervirdiff(fp, ir->eDispCorr, fr);
+ }
+}
+
+#define pr_real(fp, r) fprintf(fp, "%s: %e\n",#r, r)
+#define pr_int(fp, i) fprintf((fp), "%s: %d\n",#i, i)
+#define pr_bool(fp, b) fprintf((fp), "%s: %s\n",#b, bool_names[b])
+
+void pr_forcerec(FILE *fp, t_forcerec *fr)
+{
+ int i;
+
+ pr_real(fp, fr->rlist);
+ pr_real(fp, fr->rcoulomb);
+ pr_real(fp, fr->fudgeQQ);
+ pr_bool(fp, fr->bGrid);
+ pr_bool(fp, fr->bTwinRange);
+ /*pr_int(fp,fr->cg0);
+ pr_int(fp,fr->hcg);*/
+ for (i = 0; i < fr->nnblists; i++)
+ {
+ pr_int(fp, fr->nblists[i].table_elec_vdw.n);
+ }
+ pr_real(fp, fr->rcoulomb_switch);
+ pr_real(fp, fr->rcoulomb);
+
+ fflush(fp);
+}
+
+void forcerec_set_excl_load(t_forcerec *fr,
+ const gmx_localtop_t *top)
+{
+ const int *ind, *a;
+ int t, i, j, ntot, n, ntarget;
+
+ ind = top->excls.index;
+ a = top->excls.a;
+
+ ntot = 0;
+ for (i = 0; i < top->excls.nr; i++)
+ {
+ for (j = ind[i]; j < ind[i+1]; j++)
+ {
+ if (a[j] > i)
+ {
+ ntot++;
+ }
+ }
+ }
+
+ fr->excl_load[0] = 0;
+ n = 0;
+ i = 0;
+ for (t = 1; t <= fr->nthreads; t++)
+ {
+ ntarget = (ntot*t)/fr->nthreads;
+ while (i < top->excls.nr && n < ntarget)
+ {
+ for (j = ind[i]; j < ind[i+1]; j++)
+ {
+ if (a[j] > i)
+ {
+ n++;
+ }
+ }
+ i++;
+ }
+ fr->excl_load[t] = i;
+ }
+}
--- /dev/null
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
+ * Copyright (c) 2001-2004, The GROMACS development team.
+ * Copyright (c) 2013,2014, by the GROMACS development team, led by
+ * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+ * and including many others, as listed in the AUTHORS file in the
+ * top-level source directory and at http://www.gromacs.org.
+ *
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
+ * of the License, or (at your option) any later version.
+ *
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+ *
+ * If you want to redistribute modifications to GROMACS, please
+ * consider that scientific software is very special. Version
+ * control is crucial - bugs must be traceable. We will be happy to
+ * consider code for inclusion in the official distribution, but
+ * derived work must not be called official GROMACS. Details are found
+ * in the README & COPYING files - if they are missing, get the
+ * official version at http://www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the research papers on the package. Check out http://www.gromacs.org.
+ */
+#ifdef HAVE_CONFIG_H
+#include <config.h>
+#endif
+
+#include "typedefs.h"
+#include "gromacs/utility/cstringutil.h"
+#include "gromacs/utility/smalloc.h"
+#include "mdrun.h"
+#include "domdec.h"
+#include "mtop_util.h"
+#include "vcm.h"
+#include "nrnb.h"
+#include "macros.h"
+#include "md_logging.h"
+#include "md_support.h"
++#include "names.h"
+
+#include "gromacs/timing/wallcycle.h"
+
+/* Is the signal in one simulation independent of other simulations? */
+gmx_bool gs_simlocal[eglsNR] = { TRUE, FALSE, FALSE, TRUE };
+
+/* check which of the multisim simulations has the shortest number of
+ steps and return that number of nsteps */
+gmx_int64_t get_multisim_nsteps(const t_commrec *cr,
+ gmx_int64_t nsteps)
+{
+ gmx_int64_t steps_out;
+
+ if (MASTER(cr))
+ {
+ gmx_int64_t *buf;
+ int s;
+
+ snew(buf, cr->ms->nsim);
+
+ buf[cr->ms->sim] = nsteps;
+ gmx_sumli_sim(cr->ms->nsim, buf, cr->ms);
+
+ steps_out = -1;
+ for (s = 0; s < cr->ms->nsim; s++)
+ {
+ /* find the smallest positive number */
+ if (buf[s] >= 0 && ((steps_out < 0) || (buf[s] < steps_out)) )
+ {
+ steps_out = buf[s];
+ }
+ }
+ sfree(buf);
+
+ /* if we're the limiting simulation, don't do anything */
+ if (steps_out >= 0 && steps_out < nsteps)
+ {
+ char strbuf[255];
+ snprintf(strbuf, 255, "Will stop simulation %%d after %s steps (another simulation will end then).\n", "%"GMX_PRId64);
+ fprintf(stderr, strbuf, cr->ms->sim, steps_out);
+ }
+ }
+ /* broadcast to non-masters */
+ gmx_bcast(sizeof(gmx_int64_t), &steps_out, cr);
+ return steps_out;
+}
+
+int multisim_min(const gmx_multisim_t *ms, int nmin, int n)
+{
+ int *buf;
+ gmx_bool bPos, bEqual;
+ int s, d;
+
+ snew(buf, ms->nsim);
+ buf[ms->sim] = n;
+ gmx_sumi_sim(ms->nsim, buf, ms);
+ bPos = TRUE;
+ bEqual = TRUE;
+ for (s = 0; s < ms->nsim; s++)
+ {
+ bPos = bPos && (buf[s] > 0);
+ bEqual = bEqual && (buf[s] == buf[0]);
+ }
+ if (bPos)
+ {
+ if (bEqual)
+ {
+ nmin = min(nmin, buf[0]);
+ }
+ else
+ {
+ /* Find the least common multiple */
+ for (d = 2; d < nmin; d++)
+ {
+ s = 0;
+ while (s < ms->nsim && d % buf[s] == 0)
+ {
+ s++;
+ }
+ if (s == ms->nsim)
+ {
+ /* We found the LCM and it is less than nmin */
+ nmin = d;
+ break;
+ }
+ }
+ }
+ }
+ sfree(buf);
+
+ return nmin;
+}
+
+int multisim_nstsimsync(const t_commrec *cr,
+ const t_inputrec *ir, int repl_ex_nst)
+{
+ int nmin;
+
+ if (MASTER(cr))
+ {
+ nmin = INT_MAX;
+ nmin = multisim_min(cr->ms, nmin, ir->nstlist);
+ nmin = multisim_min(cr->ms, nmin, ir->nstcalcenergy);
+ nmin = multisim_min(cr->ms, nmin, repl_ex_nst);
+ if (nmin == INT_MAX)
+ {
+ gmx_fatal(FARGS, "Can not find an appropriate interval for inter-simulation communication, since nstlist, nstcalcenergy and -replex are all <= 0");
+ }
+ /* Avoid inter-simulation communication at every (second) step */
+ if (nmin <= 2)
+ {
+ nmin = 10;
+ }
+ }
+
+ gmx_bcast(sizeof(int), &nmin, cr);
+
+ return nmin;
+}
+
+void init_global_signals(globsig_t *gs, const t_commrec *cr,
+ const t_inputrec *ir, int repl_ex_nst)
+{
+ int i;
+
+ if (MULTISIM(cr))
+ {
+ gs->nstms = multisim_nstsimsync(cr, ir, repl_ex_nst);
+ if (debug)
+ {
+ fprintf(debug, "Syncing simulations for checkpointing and termination every %d steps\n", gs->nstms);
+ }
+ }
+ else
+ {
+ gs->nstms = 1;
+ }
+
+ for (i = 0; i < eglsNR; i++)
+ {
+ gs->sig[i] = 0;
+ gs->set[i] = 0;
+ }
+}
+
+void copy_coupling_state(t_state *statea, t_state *stateb,
+ gmx_ekindata_t *ekinda, gmx_ekindata_t *ekindb, t_grpopts* opts)
+{
+
+ /* MRS note -- might be able to get rid of some of the arguments. Look over it when it's all debugged */
+
+ int i, j, nc;
+
+ /* Make sure we have enough space for x and v */
+ if (statea->nalloc > stateb->nalloc)
+ {
+ stateb->nalloc = statea->nalloc;
+ srenew(stateb->x, stateb->nalloc);
+ srenew(stateb->v, stateb->nalloc);
+ }
+
+ stateb->natoms = statea->natoms;
+ stateb->ngtc = statea->ngtc;
+ stateb->nnhpres = statea->nnhpres;
+ stateb->veta = statea->veta;
+ if (ekinda)
+ {
+ copy_mat(ekinda->ekin, ekindb->ekin);
+ for (i = 0; i < stateb->ngtc; i++)
+ {
+ ekindb->tcstat[i].T = ekinda->tcstat[i].T;
+ ekindb->tcstat[i].Th = ekinda->tcstat[i].Th;
+ copy_mat(ekinda->tcstat[i].ekinh, ekindb->tcstat[i].ekinh);
+ copy_mat(ekinda->tcstat[i].ekinf, ekindb->tcstat[i].ekinf);
+ ekindb->tcstat[i].ekinscalef_nhc = ekinda->tcstat[i].ekinscalef_nhc;
+ ekindb->tcstat[i].ekinscaleh_nhc = ekinda->tcstat[i].ekinscaleh_nhc;
+ ekindb->tcstat[i].vscale_nhc = ekinda->tcstat[i].vscale_nhc;
+ }
+ }
+ copy_rvecn(statea->x, stateb->x, 0, stateb->natoms);
+ copy_rvecn(statea->v, stateb->v, 0, stateb->natoms);
+ copy_mat(statea->box, stateb->box);
+ copy_mat(statea->box_rel, stateb->box_rel);
+ copy_mat(statea->boxv, stateb->boxv);
+
+ for (i = 0; i < stateb->ngtc; i++)
+ {
+ nc = i*opts->nhchainlength;
+ for (j = 0; j < opts->nhchainlength; j++)
+ {
+ stateb->nosehoover_xi[nc+j] = statea->nosehoover_xi[nc+j];
+ stateb->nosehoover_vxi[nc+j] = statea->nosehoover_vxi[nc+j];
+ }
+ }
+ if (stateb->nhpres_xi != NULL)
+ {
+ for (i = 0; i < stateb->nnhpres; i++)
+ {
+ nc = i*opts->nhchainlength;
+ for (j = 0; j < opts->nhchainlength; j++)
+ {
+ stateb->nhpres_xi[nc+j] = statea->nhpres_xi[nc+j];
+ stateb->nhpres_vxi[nc+j] = statea->nhpres_vxi[nc+j];
+ }
+ }
+ }
+}
+
+real compute_conserved_from_auxiliary(t_inputrec *ir, t_state *state, t_extmass *MassQ)
+{
+ real quantity = 0;
+ switch (ir->etc)
+ {
+ case etcNO:
+ break;
+ case etcBERENDSEN:
+ break;
+ case etcNOSEHOOVER:
+ quantity = NPT_energy(ir, state, MassQ);
+ break;
+ case etcVRESCALE:
+ quantity = vrescale_energy(&(ir->opts), state->therm_integral);
+ break;
+ default:
+ break;
+ }
+ return quantity;
+}
+
+void compute_globals(FILE *fplog, gmx_global_stat_t gstat, t_commrec *cr, t_inputrec *ir,
+ t_forcerec *fr, gmx_ekindata_t *ekind,
+ t_state *state, t_state *state_global, t_mdatoms *mdatoms,
+ t_nrnb *nrnb, t_vcm *vcm, gmx_wallcycle_t wcycle,
+ gmx_enerdata_t *enerd, tensor force_vir, tensor shake_vir, tensor total_vir,
+ tensor pres, rvec mu_tot, gmx_constr_t constr,
+ globsig_t *gs, gmx_bool bInterSimGS,
+ matrix box, gmx_mtop_t *top_global,
+ gmx_bool *bSumEkinhOld, int flags)
+{
+ int i, gsi;
+ real gs_buf[eglsNR];
+ tensor corr_vir, corr_pres;
+ gmx_bool bEner, bPres, bTemp, bVV;
+ gmx_bool bRerunMD, bStopCM, bGStat, bIterate,
+ bFirstIterate, bReadEkin, bEkinAveVel, bScaleEkin, bConstrain;
+ real ekin, temp, prescorr, enercorr, dvdlcorr, dvdl_ekin;
+
+ /* translate CGLO flags to gmx_booleans */
+ bRerunMD = flags & CGLO_RERUNMD;
+ bStopCM = flags & CGLO_STOPCM;
+ bGStat = flags & CGLO_GSTAT;
+
+ bReadEkin = (flags & CGLO_READEKIN);
+ bScaleEkin = (flags & CGLO_SCALEEKIN);
+ bEner = flags & CGLO_ENERGY;
+ bTemp = flags & CGLO_TEMPERATURE;
+ bPres = (flags & CGLO_PRESSURE);
+ bConstrain = (flags & CGLO_CONSTRAINT);
+ bIterate = (flags & CGLO_ITERATE);
+ bFirstIterate = (flags & CGLO_FIRSTITERATE);
+
+ /* we calculate a full state kinetic energy either with full-step velocity verlet
+ or half step where we need the pressure */
+
+ bEkinAveVel = (ir->eI == eiVV || (ir->eI == eiVVAK && bPres) || bReadEkin);
+
+ /* in initalization, it sums the shake virial in vv, and to
+ sums ekinh_old in leapfrog (or if we are calculating ekinh_old) for other reasons */
+
+ /* ########## Kinetic energy ############## */
+
+ if (bTemp)
+ {
+ /* Non-equilibrium MD: this is parallellized, but only does communication
+ * when there really is NEMD.
+ */
+
+ if (PAR(cr) && (ekind->bNEMD))
+ {
+ accumulate_u(cr, &(ir->opts), ekind);
+ }
+ debug_gmx();
+ if (bReadEkin)
+ {
+ restore_ekinstate_from_state(cr, ekind, &state_global->ekinstate);
+ }
+ else
+ {
+
+ calc_ke_part(state, &(ir->opts), mdatoms, ekind, nrnb, bEkinAveVel, bIterate);
+ }
+
+ debug_gmx();
+ }
+
+ /* Calculate center of mass velocity if necessary, also parallellized */
+ if (bStopCM)
+ {
+ calc_vcm_grp(0, mdatoms->homenr, mdatoms,
+ state->x, state->v, vcm);
+ }
+
+ if (bTemp || bStopCM || bPres || bEner || bConstrain)
+ {
+ if (!bGStat)
+ {
+ /* We will not sum ekinh_old,
+ * so signal that we still have to do it.
+ */
+ *bSumEkinhOld = TRUE;
+
+ }
+ else
+ {
+ if (gs != NULL)
+ {
+ for (i = 0; i < eglsNR; i++)
+ {
+ gs_buf[i] = gs->sig[i];
+ }
+ }
+ if (PAR(cr))
+ {
+ wallcycle_start(wcycle, ewcMoveE);
+ global_stat(fplog, gstat, cr, enerd, force_vir, shake_vir, mu_tot,
+ ir, ekind, constr, bStopCM ? vcm : NULL,
+ gs != NULL ? eglsNR : 0, gs_buf,
+ top_global, state,
+ *bSumEkinhOld, flags);
+ wallcycle_stop(wcycle, ewcMoveE);
+ }
+ if (gs != NULL)
+ {
+ if (MULTISIM(cr) && bInterSimGS)
+ {
+ if (MASTER(cr))
+ {
+ /* Communicate the signals between the simulations */
+ gmx_sum_sim(eglsNR, gs_buf, cr->ms);
+ }
+ /* Communicate the signals form the master to the others */
+ gmx_bcast(eglsNR*sizeof(gs_buf[0]), gs_buf, cr);
+ }
+ for (i = 0; i < eglsNR; i++)
+ {
+ if (bInterSimGS || gs_simlocal[i])
+ {
+ /* Set the communicated signal only when it is non-zero,
+ * since signals might not be processed at each MD step.
+ */
+ gsi = (gs_buf[i] >= 0 ?
+ (int)(gs_buf[i] + 0.5) :
+ (int)(gs_buf[i] - 0.5));
+ if (gsi != 0)
+ {
+ gs->set[i] = gsi;
+ }
+ /* Turn off the local signal */
+ gs->sig[i] = 0;
+ }
+ }
+ }
+ *bSumEkinhOld = FALSE;
+ }
+ }
+
+ if (!ekind->bNEMD && debug && bTemp && (vcm->nr > 0))
+ {
+ correct_ekin(debug,
+ 0, mdatoms->homenr,
+ state->v, vcm->group_p[0],
+ mdatoms->massT, mdatoms->tmass, ekind->ekin);
+ }
+
+ /* Do center of mass motion removal */
+ if (bStopCM)
+ {
+ check_cm_grp(fplog, vcm, ir, 1);
+ do_stopcm_grp(0, mdatoms->homenr, mdatoms->cVCM,
+ state->x, state->v, vcm);
+ inc_nrnb(nrnb, eNR_STOPCM, mdatoms->homenr);
+ }
+
+ if (bEner)
+ {
+ /* Calculate the amplitude of the cosine velocity profile */
+ ekind->cosacc.vcos = ekind->cosacc.mvcos/mdatoms->tmass;
+ }
+
+ if (bTemp)
+ {
+ /* Sum the kinetic energies of the groups & calc temp */
+ /* compute full step kinetic energies if vv, or if vv-avek and we are computing the pressure with IR_NPT_TROTTER */
+ /* three maincase: VV with AveVel (md-vv), vv with AveEkin (md-vv-avek), leap with AveEkin (md).
+ Leap with AveVel is not supported; it's not clear that it will actually work.
+ bEkinAveVel: If TRUE, we simply multiply ekin by ekinscale to get a full step kinetic energy.
+ If FALSE, we average ekinh_old and ekinh*ekinscale_nhc to get an averaged half step kinetic energy.
+ bSaveEkinOld: If TRUE (in the case of iteration = bIterate is TRUE), we don't reset the ekinscale_nhc.
+ If FALSE, we go ahead and erase over it.
+ */
+ enerd->term[F_TEMP] = sum_ekin(&(ir->opts), ekind, &dvdl_ekin,
+ bEkinAveVel, bScaleEkin);
+ enerd->dvdl_lin[efptMASS] = (double) dvdl_ekin;
+
+ enerd->term[F_EKIN] = trace(ekind->ekin);
+ }
+
+ /* ########## Long range energy information ###### */
+
+ if (bEner || bPres || bConstrain)
+ {
+ calc_dispcorr(fplog, ir, fr, 0, top_global->natoms, box, state->lambda[efptVDW],
+ corr_pres, corr_vir, &prescorr, &enercorr, &dvdlcorr);
+ }
+
+ if (bEner && bFirstIterate)
+ {
+ enerd->term[F_DISPCORR] = enercorr;
+ enerd->term[F_EPOT] += enercorr;
+ enerd->term[F_DVDL_VDW] += dvdlcorr;
+ }
+
+ /* ########## Now pressure ############## */
+ if (bPres || bConstrain)
+ {
+
+ m_add(force_vir, shake_vir, total_vir);
+
+ /* Calculate pressure and apply LR correction if PPPM is used.
+ * Use the box from last timestep since we already called update().
+ */
+
+ enerd->term[F_PRES] = calc_pres(fr->ePBC, ir->nwall, box, ekind->ekin, total_vir, pres);
+
+ /* Calculate long range corrections to pressure and energy */
+ /* this adds to enerd->term[F_PRES] and enerd->term[F_ETOT],
+ and computes enerd->term[F_DISPCORR]. Also modifies the
+ total_vir and pres tesors */
+
+ m_add(total_vir, corr_vir, total_vir);
+ m_add(pres, corr_pres, pres);
+ enerd->term[F_PDISPCORR] = prescorr;
+ enerd->term[F_PRES] += prescorr;
+ }
+}
+
+void check_nst_param(FILE *fplog, t_commrec *cr,
+ const char *desc_nst, int nst,
+ const char *desc_p, int *p)
+{
+ if (*p > 0 && *p % nst != 0)
+ {
+ /* Round up to the next multiple of nst */
+ *p = ((*p)/nst + 1)*nst;
+ md_print_warn(cr, fplog,
+ "NOTE: %s changes %s to %d\n", desc_nst, desc_p, *p);
+ }
+}
+
+void set_current_lambdas(gmx_int64_t step, t_lambda *fepvals, gmx_bool bRerunMD,
+ t_trxframe *rerun_fr, t_state *state_global, t_state *state, double lam0[])
+/* find the current lambdas. If rerunning, we either read in a state, or a lambda value,
+ requiring different logic. */
+{
+ real frac;
+ int i, fep_state = 0;
+ if (bRerunMD)
+ {
+ if (rerun_fr->bLambda)
+ {
+ if (fepvals->delta_lambda == 0)
+ {
+ state_global->lambda[efptFEP] = rerun_fr->lambda;
+ for (i = 0; i < efptNR; i++)
+ {
+ if (i != efptFEP)
+ {
+ state->lambda[i] = state_global->lambda[i];
+ }
+ }
+ }
+ else
+ {
+ /* find out between which two value of lambda we should be */
+ frac = (step*fepvals->delta_lambda);
+ fep_state = floor(frac*fepvals->n_lambda);
+ /* interpolate between this state and the next */
+ /* this assumes that the initial lambda corresponds to lambda==0, which is verified in grompp */
+ frac = (frac*fepvals->n_lambda)-fep_state;
+ for (i = 0; i < efptNR; i++)
+ {
+ state_global->lambda[i] = lam0[i] + (fepvals->all_lambda[i][fep_state]) +
+ frac*(fepvals->all_lambda[i][fep_state+1]-fepvals->all_lambda[i][fep_state]);
+ }
+ }
+ }
+ else if (rerun_fr->bFepState)
+ {
+ state_global->fep_state = rerun_fr->fep_state;
+ for (i = 0; i < efptNR; i++)
+ {
+ state_global->lambda[i] = fepvals->all_lambda[i][fep_state];
+ }
+ }
+ }
+ else
+ {
+ if (fepvals->delta_lambda != 0)
+ {
+ /* find out between which two value of lambda we should be */
+ frac = (step*fepvals->delta_lambda);
+ if (fepvals->n_lambda > 0)
+ {
+ fep_state = floor(frac*fepvals->n_lambda);
+ /* interpolate between this state and the next */
+ /* this assumes that the initial lambda corresponds to lambda==0, which is verified in grompp */
+ frac = (frac*fepvals->n_lambda)-fep_state;
+ for (i = 0; i < efptNR; i++)
+ {
+ state_global->lambda[i] = lam0[i] + (fepvals->all_lambda[i][fep_state]) +
+ frac*(fepvals->all_lambda[i][fep_state+1]-fepvals->all_lambda[i][fep_state]);
+ }
+ }
+ else
+ {
+ for (i = 0; i < efptNR; i++)
+ {
+ state_global->lambda[i] = lam0[i] + frac;
+ }
+ }
+ }
+ else
+ {
+ if (state->fep_state > 0)
+ {
+ state_global->fep_state = state->fep_state; /* state->fep is the one updated by bExpanded */
+ for (i = 0; i < efptNR; i++)
+ {
+ state_global->lambda[i] = fepvals->all_lambda[i][state_global->fep_state];
+ }
+ }
+ }
+ }
+ for (i = 0; i < efptNR; i++)
+ {
+ state->lambda[i] = state_global->lambda[i];
+ }
+}
+
+static void min_zero(int *n, int i)
+{
+ if (i > 0 && (*n == 0 || i < *n))
+ {
+ *n = i;
+ }
+}
+
+static int lcd4(int i1, int i2, int i3, int i4)
+{
+ int nst;
+
+ nst = 0;
+ min_zero(&nst, i1);
+ min_zero(&nst, i2);
+ min_zero(&nst, i3);
+ min_zero(&nst, i4);
+ if (nst == 0)
+ {
+ gmx_incons("All 4 inputs for determininig nstglobalcomm are <= 0");
+ }
+
+ while (nst > 1 && ((i1 > 0 && i1 % nst != 0) ||
+ (i2 > 0 && i2 % nst != 0) ||
+ (i3 > 0 && i3 % nst != 0) ||
+ (i4 > 0 && i4 % nst != 0)))
+ {
+ nst--;
+ }
+
+ return nst;
+}
+
+int check_nstglobalcomm(FILE *fplog, t_commrec *cr,
+ int nstglobalcomm, t_inputrec *ir)
+{
+ if (!EI_DYNAMICS(ir->eI))
+ {
+ nstglobalcomm = 1;
+ }
+
+ if (nstglobalcomm == -1)
+ {
+ if (!(ir->nstcalcenergy > 0 ||
+ ir->nstlist > 0 ||
+ ir->etc != etcNO ||
+ ir->epc != epcNO))
+ {
+ nstglobalcomm = 10;
+ if (ir->nstenergy > 0 && ir->nstenergy < nstglobalcomm)
+ {
+ nstglobalcomm = ir->nstenergy;
+ }
+ }
+ else
+ {
+ /* Ensure that we do timely global communication for
+ * (possibly) each of the four following options.
+ */
+ nstglobalcomm = lcd4(ir->nstcalcenergy,
+ ir->nstlist,
+ ir->etc != etcNO ? ir->nsttcouple : 0,
+ ir->epc != epcNO ? ir->nstpcouple : 0);
+ }
+ }
+ else
+ {
+ if (ir->nstlist > 0 &&
+ nstglobalcomm > ir->nstlist && nstglobalcomm % ir->nstlist != 0)
+ {
+ nstglobalcomm = (nstglobalcomm / ir->nstlist)*ir->nstlist;
+ md_print_warn(cr, fplog, "WARNING: nstglobalcomm is larger than nstlist, but not a multiple, setting it to %d\n", nstglobalcomm);
+ }
+ if (ir->nstcalcenergy > 0)
+ {
+ check_nst_param(fplog, cr, "-gcom", nstglobalcomm,
+ "nstcalcenergy", &ir->nstcalcenergy);
+ }
+ if (ir->etc != etcNO && ir->nsttcouple > 0)
+ {
+ check_nst_param(fplog, cr, "-gcom", nstglobalcomm,
+ "nsttcouple", &ir->nsttcouple);
+ }
+ if (ir->epc != epcNO && ir->nstpcouple > 0)
+ {
+ check_nst_param(fplog, cr, "-gcom", nstglobalcomm,
+ "nstpcouple", &ir->nstpcouple);
+ }
+
+ check_nst_param(fplog, cr, "-gcom", nstglobalcomm,
+ "nstenergy", &ir->nstenergy);
+
+ check_nst_param(fplog, cr, "-gcom", nstglobalcomm,
+ "nstlog", &ir->nstlog);
+ }
+
+ if (ir->comm_mode != ecmNO && ir->nstcomm < nstglobalcomm)
+ {
+ md_print_warn(cr, fplog, "WARNING: Changing nstcomm from %d to %d\n",
+ ir->nstcomm, nstglobalcomm);
+ ir->nstcomm = nstglobalcomm;
+ }
+
+ return nstglobalcomm;
+}
+
+void check_ir_old_tpx_versions(t_commrec *cr, FILE *fplog,
+ t_inputrec *ir, gmx_mtop_t *mtop)
+{
+ /* Check required for old tpx files */
+ if (IR_TWINRANGE(*ir) && ir->nstlist > 1 &&
+ ir->nstcalcenergy % ir->nstlist != 0)
+ {
+ md_print_warn(cr, fplog, "Old tpr file with twin-range settings: modifying energy calculation and/or T/P-coupling frequencies\n");
+
+ if (gmx_mtop_ftype_count(mtop, F_CONSTR) +
+ gmx_mtop_ftype_count(mtop, F_CONSTRNC) > 0 &&
+ ir->eConstrAlg == econtSHAKE)
+ {
+ md_print_warn(cr, fplog, "With twin-range cut-off's and SHAKE the virial and pressure are incorrect\n");
+ if (ir->epc != epcNO)
+ {
+ gmx_fatal(FARGS, "Can not do pressure coupling with twin-range cut-off's and SHAKE");
+ }
+ }
+ check_nst_param(fplog, cr, "nstlist", ir->nstlist,
+ "nstcalcenergy", &ir->nstcalcenergy);
+ if (ir->epc != epcNO)
+ {
+ check_nst_param(fplog, cr, "nstlist", ir->nstlist,
+ "nstpcouple", &ir->nstpcouple);
+ }
+ check_nst_param(fplog, cr, "nstcalcenergy", ir->nstcalcenergy,
+ "nstenergy", &ir->nstenergy);
+ check_nst_param(fplog, cr, "nstcalcenergy", ir->nstcalcenergy,
+ "nstlog", &ir->nstlog);
+ if (ir->efep != efepNO)
+ {
+ check_nst_param(fplog, cr, "nstcalcenergy", ir->nstcalcenergy,
+ "nstdhdl", &ir->fepvals->nstdhdl);
+ }
+ }
++
++ if (EI_VV(ir->eI) && IR_TWINRANGE(*ir) && ir->nstlist > 1)
++ {
++ gmx_fatal(FARGS, "Twin-range multiple time stepping does not work with integrator %s.", ei_names[ir->eI]);
++ }
+}
+
+void rerun_parallel_comm(t_commrec *cr, t_trxframe *fr,
+ gmx_bool *bNotLastFrame)
+{
+ gmx_bool bAlloc;
+ rvec *xp, *vp;
+
+ bAlloc = (fr->natoms == 0);
+
+ if (MASTER(cr) && !*bNotLastFrame)
+ {
+ fr->natoms = -1;
+ }
+ xp = fr->x;
+ vp = fr->v;
+ gmx_bcast(sizeof(*fr), fr, cr);
+ fr->x = xp;
+ fr->v = vp;
+
+ *bNotLastFrame = (fr->natoms >= 0);
+
+}
--- /dev/null
- gmx_fatal(FARGS, "Distance between pull groups %d and %d (%f nm) is larger than 0.49 times the box size (%f)",
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
+ * Copyright (c) 2001-2004, The GROMACS development team.
+ * Copyright (c) 2013,2014, by the GROMACS development team, led by
+ * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+ * and including many others, as listed in the AUTHORS file in the
+ * top-level source directory and at http://www.gromacs.org.
+ *
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
+ * of the License, or (at your option) any later version.
+ *
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+ *
+ * If you want to redistribute modifications to GROMACS, please
+ * consider that scientific software is very special. Version
+ * control is crucial - bugs must be traceable. We will be happy to
+ * consider code for inclusion in the official distribution, but
+ * derived work must not be called official GROMACS. Details are found
+ * in the README & COPYING files - if they are missing, get the
+ * official version at http://www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the research papers on the package. Check out http://www.gromacs.org.
+ */
+#ifdef HAVE_CONFIG_H
+#include <config.h>
+#endif
+
+
+#include <math.h>
+#include <stdio.h>
+#include <stdlib.h>
+#include "gromacs/fileio/futil.h"
+#include "index.h"
+#include "gromacs/fileio/gmxfio.h"
+#include "vec.h"
+#include "typedefs.h"
+#include "types/commrec.h"
+#include "network.h"
+#include "gromacs/fileio/filenm.h"
+#include <string.h>
+#include "gromacs/utility/smalloc.h"
+#include "pull.h"
+#include "xvgr.h"
+#include "names.h"
+#include "pbc.h"
+#include "mtop_util.h"
+#include "mdrun.h"
+#include "gmx_ga2la.h"
+#include "copyrite.h"
+#include "macros.h"
+#include "vec.h"
+
+static void pull_print_group_x(FILE *out, ivec dim, const t_pull_group *pgrp)
+{
+ int m;
+
+ for (m = 0; m < DIM; m++)
+ {
+ if (dim[m])
+ {
+ fprintf(out, "\t%g", pgrp->x[m]);
+ }
+ }
+}
+
+static void pull_print_coord_dr(FILE *out, ivec dim, const t_pull_coord *pcrd)
+{
+ int m;
+
+ for (m = 0; m < DIM; m++)
+ {
+ if (dim[m])
+ {
+ fprintf(out, "\t%g", pcrd->dr[m]);
+ }
+ }
+}
+
+static void pull_print_x(FILE *out, t_pull *pull, double t)
+{
+ int c;
+ const t_pull_coord *pcrd;
+
+ fprintf(out, "%.4f", t);
+
+ for (c = 0; c < pull->ncoord; c++)
+ {
+ pcrd = &pull->coord[c];
+
+ if (pull->bPrintRef)
+ {
+ if (PULL_CYL(pull))
+ {
+ pull_print_group_x(out, pull->dim, &pull->dyna[c]);
+ }
+ else
+ {
+ pull_print_group_x(out, pull->dim, &pull->group[pcrd->group[0]]);
+ }
+ }
+ pull_print_coord_dr(out, pull->dim, pcrd);
+ }
+ fprintf(out, "\n");
+}
+
+static void pull_print_f(FILE *out, t_pull *pull, double t)
+{
+ int c, d;
+
+ fprintf(out, "%.4f", t);
+
+ for (c = 0; c < pull->ncoord; c++)
+ {
+ fprintf(out, "\t%g", pull->coord[c].f_scal);
+ }
+ fprintf(out, "\n");
+}
+
+void pull_print_output(t_pull *pull, gmx_int64_t step, double time)
+{
+ if ((pull->nstxout != 0) && (step % pull->nstxout == 0))
+ {
+ pull_print_x(pull->out_x, pull, time);
+ }
+
+ if ((pull->nstfout != 0) && (step % pull->nstfout == 0))
+ {
+ pull_print_f(pull->out_f, pull, time);
+ }
+}
+
+static FILE *open_pull_out(const char *fn, t_pull *pull, const output_env_t oenv,
+ gmx_bool bCoord, unsigned long Flags)
+{
+ FILE *fp;
+ int nsets, c, m;
+ char **setname, buf[10];
+
+ if (Flags & MD_APPENDFILES)
+ {
+ fp = gmx_fio_fopen(fn, "a+");
+ }
+ else
+ {
+ fp = gmx_fio_fopen(fn, "w+");
+ if (bCoord)
+ {
+ xvgr_header(fp, "Pull COM", "Time (ps)", "Position (nm)",
+ exvggtXNY, oenv);
+ }
+ else
+ {
+ xvgr_header(fp, "Pull force", "Time (ps)", "Force (kJ/mol/nm)",
+ exvggtXNY, oenv);
+ }
+
+ snew(setname, 2*pull->ncoord*DIM);
+ nsets = 0;
+ for (c = 0; c < pull->ncoord; c++)
+ {
+ if (bCoord)
+ {
+ if (pull->bPrintRef)
+ {
+ for (m = 0; m < DIM; m++)
+ {
+ if (pull->dim[m])
+ {
+ sprintf(buf, "%d %s%c", c+1, "c", 'X'+m);
+ setname[nsets] = strdup(buf);
+ nsets++;
+ }
+ }
+ }
+ for (m = 0; m < DIM; m++)
+ {
+ if (pull->dim[m])
+ {
+ sprintf(buf, "%d %s%c", c+1, "d", 'X'+m);
+ setname[nsets] = strdup(buf);
+ nsets++;
+ }
+ }
+ }
+ else
+ {
+ sprintf(buf, "%d", c+1);
+ setname[nsets] = strdup(buf);
+ nsets++;
+ }
+ }
+ if (nsets > 1)
+ {
+ xvgr_legend(fp, nsets, (const char**)setname, oenv);
+ }
+ for (c = 0; c < nsets; c++)
+ {
+ sfree(setname[c]);
+ }
+ sfree(setname);
+ }
+
+ return fp;
+}
+
+/* Apply forces in a mass weighted fashion */
+static void apply_forces_grp(const t_pull_group *pgrp, const t_mdatoms *md,
+ const dvec f_pull, int sign, rvec *f)
+{
+ int i, ii, m;
+ double wmass, inv_wm;
+
+ inv_wm = pgrp->wscale*pgrp->invtm;
+
+ for (i = 0; i < pgrp->nat_loc; i++)
+ {
+ ii = pgrp->ind_loc[i];
+ wmass = md->massT[ii];
+ if (pgrp->weight_loc)
+ {
+ wmass *= pgrp->weight_loc[i];
+ }
+
+ for (m = 0; m < DIM; m++)
+ {
+ f[ii][m] += sign * wmass * f_pull[m] * inv_wm;
+ }
+ }
+}
+
+/* Apply forces in a mass weighted fashion */
+static void apply_forces(t_pull * pull, t_mdatoms * md, rvec *f)
+{
+ int c;
+ const t_pull_coord *pcrd;
+
+ for (c = 0; c < pull->ncoord; c++)
+ {
+ pcrd = &pull->coord[c];
+
+ if (PULL_CYL(pull))
+ {
+ apply_forces_grp(&pull->dyna[c], md, pcrd->f, -1, f);
+ }
+ else
+ {
+ if (pull->group[pcrd->group[0]].nat > 0)
+ {
+ apply_forces_grp(&pull->group[pcrd->group[0]], md, pcrd->f, -1, f);
+ }
+ }
+ apply_forces_grp(&pull->group[pcrd->group[1]], md, pcrd->f, 1, f);
+ }
+}
+
+static double max_pull_distance2(const t_pull *pull, const t_pbc *pbc)
+{
+ double max_d2;
+ int m;
+
+ max_d2 = GMX_DOUBLE_MAX;
+
+ if (pull->eGeom != epullgDIRPBC)
+ {
+ for (m = 0; m < pbc->ndim_ePBC; m++)
+ {
+ if (pull->dim[m] != 0)
+ {
+ max_d2 = min(max_d2, norm2(pbc->box[m]));
+ }
+ }
+ }
+
+ return 0.25*max_d2;
+}
+
+static void low_get_pull_coord_dr(const t_pull *pull,
+ const t_pull_coord *pcrd,
+ const t_pbc *pbc, double t,
+ dvec xg, dvec xref, double max_dist2,
+ dvec dr)
+{
+ const t_pull_group *pgrp0, *pgrp1;
+ int m;
+ dvec xrefr, dref = {0, 0, 0};
+ double dr2;
+
+ pgrp0 = &pull->group[pcrd->group[0]];
+ pgrp1 = &pull->group[pcrd->group[1]];
+
+ /* Only the first group can be an absolute reference, in that case nat=0 */
+ if (pgrp0->nat == 0)
+ {
+ for (m = 0; m < DIM; m++)
+ {
+ xref[m] = pcrd->origin[m];
+ }
+ }
+
+ copy_dvec(xref, xrefr);
+
+ if (pull->eGeom == epullgDIRPBC)
+ {
+ for (m = 0; m < DIM; m++)
+ {
+ dref[m] = (pcrd->init + pcrd->rate*t)*pcrd->vec[m];
+ }
+ /* Add the reference position, so we use the correct periodic image */
+ dvec_inc(xrefr, dref);
+ }
+
+ pbc_dx_d(pbc, xg, xrefr, dr);
+ dr2 = 0;
+ for (m = 0; m < DIM; m++)
+ {
+ dr[m] *= pull->dim[m];
+ dr2 += dr[m]*dr[m];
+ }
+ if (max_dist2 >= 0 && dr2 > 0.98*0.98*max_dist2)
+ {
++ gmx_fatal(FARGS, "Distance between pull groups %d and %d (%f nm) is larger than 0.49 times the box size (%f).\nYou might want to consider using \"pull-geometry = direction-periodic\" instead.\n",
+ pcrd->group[0], pcrd->group[1], sqrt(dr2), sqrt(max_dist2));
+ }
+
+ if (pull->eGeom == epullgDIRPBC)
+ {
+ dvec_inc(dr, dref);
+ }
+}
+
+static void get_pull_coord_dr(const t_pull *pull,
+ int coord_ind,
+ const t_pbc *pbc, double t,
+ dvec dr)
+{
+ double md2;
+ const t_pull_coord *pcrd;
+
+ if (pull->eGeom == epullgDIRPBC)
+ {
+ md2 = -1;
+ }
+ else
+ {
+ md2 = max_pull_distance2(pull, pbc);
+ }
+
+ pcrd = &pull->coord[coord_ind];
+
+ low_get_pull_coord_dr(pull, pcrd, pbc, t,
+ pull->group[pcrd->group[1]].x,
+ PULL_CYL(pull) ? pull->dyna[coord_ind].x : pull->group[pcrd->group[0]].x,
+ md2,
+ dr);
+}
+
+void get_pull_coord_distance(const t_pull *pull,
+ int coord_ind,
+ const t_pbc *pbc, double t,
+ dvec dr, double *dev)
+{
+ static gmx_bool bWarned = FALSE; /* TODO: this should be fixed for thread-safety,
+ but is fairly benign */
+ const t_pull_coord *pcrd;
+ int m;
+ double ref, drs, inpr;
+
+ pcrd = &pull->coord[coord_ind];
+
+ get_pull_coord_dr(pull, coord_ind, pbc, t, dr);
+
+ ref = pcrd->init + pcrd->rate*t;
+
+ switch (pull->eGeom)
+ {
+ case epullgDIST:
+ /* Pull along the vector between the com's */
+ if (ref < 0 && !bWarned)
+ {
+ fprintf(stderr, "\nPull reference distance for coordinate %d is negative (%f)\n", coord_ind+1, ref);
+ bWarned = TRUE;
+ }
+ drs = dnorm(dr);
+ if (drs == 0)
+ {
+ /* With no vector we can not determine the direction for the force,
+ * so we set the force to zero.
+ */
+ *dev = 0;
+ }
+ else
+ {
+ /* Determine the deviation */
+ *dev = drs - ref;
+ }
+ break;
+ case epullgDIR:
+ case epullgDIRPBC:
+ case epullgCYL:
+ /* Pull along vec */
+ inpr = 0;
+ for (m = 0; m < DIM; m++)
+ {
+ inpr += pcrd->vec[m]*dr[m];
+ }
+ *dev = inpr - ref;
+ break;
+ }
+}
+
+void clear_pull_forces(t_pull *pull)
+{
+ int i;
+
+ /* Zeroing the forces is only required for constraint pulling.
+ * It can happen that multiple constraint steps need to be applied
+ * and therefore the constraint forces need to be accumulated.
+ */
+ for (i = 0; i < pull->ncoord; i++)
+ {
+ clear_dvec(pull->coord[i].f);
+ pull->coord[i].f_scal = 0;
+ }
+}
+
+/* Apply constraint using SHAKE */
+static void do_constraint(t_pull *pull, t_pbc *pbc,
+ rvec *x, rvec *v,
+ gmx_bool bMaster, tensor vir,
+ double dt, double t)
+{
+
+ dvec *r_ij; /* x[i] com of i in prev. step. Obeys constr. -> r_ij[i] */
+ dvec unc_ij; /* xp[i] com of i this step, before constr. -> unc_ij */
+ dvec *rnew; /* current 'new' positions of the groups */
+ double *dr_tot; /* the total update of the coords */
+ double ref;
+ dvec vec;
+ double d0, inpr;
+ double lambda, rm, mass, invdt = 0;
+ gmx_bool bConverged_all, bConverged = FALSE;
+ int niter = 0, g, c, ii, j, m, max_iter = 100;
+ double a;
+ dvec f; /* the pull force */
+ dvec tmp, tmp3;
+ t_pull_group *pdyna, *pgrp0, *pgrp1;
+ t_pull_coord *pcrd;
+
+ snew(r_ij, pull->ncoord);
+ snew(dr_tot, pull->ncoord);
+
+ snew(rnew, pull->ngroup);
+
+ /* copy the current unconstrained positions for use in iterations. We
+ iterate until rinew[i] and rjnew[j] obey the constraints. Then
+ rinew - pull.x_unc[i] is the correction dr to group i */
+ for (g = 0; g < pull->ngroup; g++)
+ {
+ copy_dvec(pull->group[g].xp, rnew[g]);
+ }
+ if (PULL_CYL(pull))
+ {
+ /* There is only one pull coordinate and reference group */
+ copy_dvec(pull->dyna[0].xp, rnew[pull->coord[0].group[0]]);
+ }
+
+ /* Determine the constraint directions from the old positions */
+ for (c = 0; c < pull->ncoord; c++)
+ {
+ get_pull_coord_dr(pull, c, pbc, t, r_ij[c]);
+ /* Store the difference vector at time t for printing */
+ copy_dvec(r_ij[c], pull->coord[c].dr);
+ if (debug)
+ {
+ fprintf(debug, "Pull coord %d dr %f %f %f\n",
+ c, r_ij[c][XX], r_ij[c][YY], r_ij[c][ZZ]);
+ }
+
+ if (pull->eGeom == epullgDIR || pull->eGeom == epullgDIRPBC)
+ {
+ /* Select the component along vec */
+ a = 0;
+ for (m = 0; m < DIM; m++)
+ {
+ a += pull->coord[c].vec[m]*r_ij[c][m];
+ }
+ for (m = 0; m < DIM; m++)
+ {
+ r_ij[c][m] = a*pull->coord[c].vec[m];
+ }
+ }
+ }
+
+ bConverged_all = FALSE;
+ while (!bConverged_all && niter < max_iter)
+ {
+ bConverged_all = TRUE;
+
+ /* loop over all constraints */
+ for (c = 0; c < pull->ncoord; c++)
+ {
+ dvec dr0, dr1;
+
+ pcrd = &pull->coord[c];
+ pgrp0 = &pull->group[pcrd->group[0]];
+ pgrp1 = &pull->group[pcrd->group[1]];
+
+ /* Get the current difference vector */
+ low_get_pull_coord_dr(pull, pcrd, pbc, t,
+ rnew[pcrd->group[1]],
+ rnew[pcrd->group[0]],
+ -1, unc_ij);
+
+ ref = pcrd->init + pcrd->rate*t;
+
+ if (debug)
+ {
+ fprintf(debug, "Pull coord %d, iteration %d\n", c, niter);
+ }
+
+ rm = 1.0/(pgrp0->invtm + pgrp1->invtm);
+
+ switch (pull->eGeom)
+ {
+ case epullgDIST:
+ if (ref <= 0)
+ {
+ gmx_fatal(FARGS, "The pull constraint reference distance for group %d is <= 0 (%f)", c, ref);
+ }
+
+ {
+ double q, c_a, c_b, c_c;
+
+ c_a = diprod(r_ij[c], r_ij[c]);
+ c_b = diprod(unc_ij, r_ij[c])*2;
+ c_c = diprod(unc_ij, unc_ij) - dsqr(ref);
+
+ if (c_b < 0)
+ {
+ q = -0.5*(c_b - sqrt(c_b*c_b - 4*c_a*c_c));
+ lambda = -q/c_a;
+ }
+ else
+ {
+ q = -0.5*(c_b + sqrt(c_b*c_b - 4*c_a*c_c));
+ lambda = -c_c/q;
+ }
+
+ if (debug)
+ {
+ fprintf(debug,
+ "Pull ax^2+bx+c=0: a=%e b=%e c=%e lambda=%e\n",
+ c_a, c_b, c_c, lambda);
+ }
+ }
+
+ /* The position corrections dr due to the constraints */
+ dsvmul(-lambda*rm*pgrp1->invtm, r_ij[c], dr1);
+ dsvmul( lambda*rm*pgrp0->invtm, r_ij[c], dr0);
+ dr_tot[c] += -lambda*dnorm(r_ij[c]);
+ break;
+ case epullgDIR:
+ case epullgDIRPBC:
+ case epullgCYL:
+ /* A 1-dimensional constraint along a vector */
+ a = 0;
+ for (m = 0; m < DIM; m++)
+ {
+ vec[m] = pcrd->vec[m];
+ a += unc_ij[m]*vec[m];
+ }
+ /* Select only the component along the vector */
+ dsvmul(a, vec, unc_ij);
+ lambda = a - ref;
+ if (debug)
+ {
+ fprintf(debug, "Pull inpr %e lambda: %e\n", a, lambda);
+ }
+
+ /* The position corrections dr due to the constraints */
+ dsvmul(-lambda*rm*pgrp1->invtm, vec, dr1);
+ dsvmul( lambda*rm*pgrp0->invtm, vec, dr0);
+ dr_tot[c] += -lambda;
+ break;
+ }
+
+ /* DEBUG */
+ if (debug)
+ {
+ int g0, g1;
+
+ g0 = pcrd->group[0];
+ g1 = pcrd->group[1];
+ low_get_pull_coord_dr(pull, pcrd, pbc, t, rnew[g1], rnew[g0], -1, tmp);
+ low_get_pull_coord_dr(pull, pcrd, pbc, t, dr1, dr0, -1, tmp3);
+ fprintf(debug,
+ "Pull cur %8.5f %8.5f %8.5f j:%8.5f %8.5f %8.5f d: %8.5f\n",
+ rnew[g0][0], rnew[g0][1], rnew[g0][2],
+ rnew[g1][0], rnew[g1][1], rnew[g1][2], dnorm(tmp));
+ fprintf(debug,
+ "Pull ref %8s %8s %8s %8s %8s %8s d: %8.5f\n",
+ "", "", "", "", "", "", ref);
+ fprintf(debug,
+ "Pull cor %8.5f %8.5f %8.5f j:%8.5f %8.5f %8.5f d: %8.5f\n",
+ dr0[0], dr0[1], dr0[2],
+ dr1[0], dr1[1], dr1[2],
+ dnorm(tmp3));
+ } /* END DEBUG */
+
+ /* Update the COMs with dr */
+ dvec_inc(rnew[pcrd->group[1]], dr1);
+ dvec_inc(rnew[pcrd->group[0]], dr0);
+ }
+
+ /* Check if all constraints are fullfilled now */
+ for (c = 0; c < pull->ncoord; c++)
+ {
+ pcrd = &pull->coord[c];
+
+ low_get_pull_coord_dr(pull, pcrd, pbc, t,
+ rnew[pcrd->group[1]],
+ rnew[pcrd->group[0]],
+ -1, unc_ij);
+
+ switch (pull->eGeom)
+ {
+ case epullgDIST:
+ bConverged = fabs(dnorm(unc_ij) - ref) < pull->constr_tol;
+ break;
+ case epullgDIR:
+ case epullgDIRPBC:
+ case epullgCYL:
+ for (m = 0; m < DIM; m++)
+ {
+ vec[m] = pcrd->vec[m];
+ }
+ inpr = diprod(unc_ij, vec);
+ dsvmul(inpr, vec, unc_ij);
+ bConverged =
+ fabs(diprod(unc_ij, vec) - ref) < pull->constr_tol;
+ break;
+ }
+
+ if (!bConverged)
+ {
+ if (debug)
+ {
+ fprintf(debug, "NOT CONVERGED YET: Group %d:"
+ "d_ref = %f, current d = %f\n",
+ g, ref, dnorm(unc_ij));
+ }
+
+ bConverged_all = FALSE;
+ }
+ }
+
+ niter++;
+ /* if after all constraints are dealt with and bConverged is still TRUE
+ we're finished, if not we do another iteration */
+ }
+ if (niter > max_iter)
+ {
+ gmx_fatal(FARGS, "Too many iterations for constraint run: %d", niter);
+ }
+
+ /* DONE ITERATING, NOW UPDATE COORDINATES AND CALC. CONSTRAINT FORCES */
+
+ if (v)
+ {
+ invdt = 1/dt;
+ }
+
+ /* update atoms in the groups */
+ for (g = 0; g < pull->ngroup; g++)
+ {
+ const t_pull_group *pgrp;
+ dvec dr;
+
+ if (PULL_CYL(pull) && g == pull->coord[0].group[0])
+ {
+ pgrp = &pull->dyna[0];
+ }
+ else
+ {
+ pgrp = &pull->group[g];
+ }
+
+ /* get the final constraint displacement dr for group g */
+ dvec_sub(rnew[g], pgrp->xp, dr);
+ /* select components of dr */
+ for (m = 0; m < DIM; m++)
+ {
+ dr[m] *= pull->dim[m];
+ }
+
+ /* update the atom positions */
+ copy_dvec(dr, tmp);
+ for (j = 0; j < pgrp->nat_loc; j++)
+ {
+ ii = pgrp->ind_loc[j];
+ if (pgrp->weight_loc)
+ {
+ dsvmul(pgrp->wscale*pgrp->weight_loc[j], dr, tmp);
+ }
+ for (m = 0; m < DIM; m++)
+ {
+ x[ii][m] += tmp[m];
+ }
+ if (v)
+ {
+ for (m = 0; m < DIM; m++)
+ {
+ v[ii][m] += invdt*tmp[m];
+ }
+ }
+ }
+ }
+
+ /* calculate the constraint forces, used for output and virial only */
+ for (c = 0; c < pull->ncoord; c++)
+ {
+ pcrd = &pull->coord[c];
+ pcrd->f_scal = dr_tot[c]/((pull->group[pcrd->group[0]].invtm + pull->group[pcrd->group[1]].invtm)*dt*dt);
+
+ if (vir && bMaster)
+ {
+ double f_invr;
+
+ /* Add the pull contribution to the virial */
+ f_invr = pcrd->f_scal/dnorm(r_ij[c]);
+
+ for (j = 0; j < DIM; j++)
+ {
+ for (m = 0; m < DIM; m++)
+ {
+ vir[j][m] -= 0.5*f_invr*r_ij[c][j]*r_ij[c][m];
+ }
+ }
+ }
+ }
+
+ /* finished! I hope. Give back some memory */
+ sfree(r_ij);
+ sfree(dr_tot);
+ sfree(rnew);
+}
+
+/* Pulling with a harmonic umbrella potential or constant force */
+static void do_pull_pot(int ePull,
+ t_pull *pull, t_pbc *pbc, double t, real lambda,
+ real *V, tensor vir, real *dVdl)
+{
+ int c, j, m;
+ double dev, ndr, invdr;
+ real k, dkdl;
+ t_pull_coord *pcrd;
+
+ /* loop over the pull coordinates */
+ *V = 0;
+ *dVdl = 0;
+ for (c = 0; c < pull->ncoord; c++)
+ {
+ pcrd = &pull->coord[c];
+
+ get_pull_coord_distance(pull, c, pbc, t, pcrd->dr, &dev);
+
+ k = (1.0 - lambda)*pcrd->k + lambda*pcrd->kB;
+ dkdl = pcrd->kB - pcrd->k;
+
+ switch (pull->eGeom)
+ {
+ case epullgDIST:
+ ndr = dnorm(pcrd->dr);
+ invdr = 1/ndr;
+ if (ePull == epullUMBRELLA)
+ {
+ pcrd->f_scal = -k*dev;
+ *V += 0.5* k*dsqr(dev);
+ *dVdl += 0.5*dkdl*dsqr(dev);
+ }
+ else
+ {
+ pcrd->f_scal = -k;
+ *V += k*ndr;
+ *dVdl += dkdl*ndr;
+ }
+ for (m = 0; m < DIM; m++)
+ {
+ pcrd->f[m] = pcrd->f_scal*pcrd->dr[m]*invdr;
+ }
+ break;
+ case epullgDIR:
+ case epullgDIRPBC:
+ case epullgCYL:
+ if (ePull == epullUMBRELLA)
+ {
+ pcrd->f_scal = -k*dev;
+ *V += 0.5* k*dsqr(dev);
+ *dVdl += 0.5*dkdl*dsqr(dev);
+ }
+ else
+ {
+ ndr = 0;
+ for (m = 0; m < DIM; m++)
+ {
+ ndr += pcrd->vec[m]*pcrd->dr[m];
+ }
+ pcrd->f_scal = -k;
+ *V += k*ndr;
+ *dVdl += dkdl*ndr;
+ }
+ for (m = 0; m < DIM; m++)
+ {
+ pcrd->f[m] = pcrd->f_scal*pcrd->vec[m];
+ }
+ break;
+ }
+
+ if (vir)
+ {
+ /* Add the pull contribution to the virial */
+ for (j = 0; j < DIM; j++)
+ {
+ for (m = 0; m < DIM; m++)
+ {
+ vir[j][m] -= 0.5*pcrd->f[j]*pcrd->dr[m];
+ }
+ }
+ }
+ }
+}
+
+real pull_potential(int ePull, t_pull *pull, t_mdatoms *md, t_pbc *pbc,
+ t_commrec *cr, double t, real lambda,
+ rvec *x, rvec *f, tensor vir, real *dvdlambda)
+{
+ real V, dVdl;
+
+ pull_calc_coms(cr, pull, md, pbc, t, x, NULL);
+
+ do_pull_pot(ePull, pull, pbc, t, lambda,
+ &V, pull->bVirial && MASTER(cr) ? vir : NULL, &dVdl);
+
+ /* Distribute forces over pulled groups */
+ apply_forces(pull, md, f);
+
+ if (MASTER(cr))
+ {
+ *dvdlambda += dVdl;
+ }
+
+ return (MASTER(cr) ? V : 0.0);
+}
+
+void pull_constraint(t_pull *pull, t_mdatoms *md, t_pbc *pbc,
+ t_commrec *cr, double dt, double t,
+ rvec *x, rvec *xp, rvec *v, tensor vir)
+{
+ pull_calc_coms(cr, pull, md, pbc, t, x, xp);
+
+ do_constraint(pull, pbc, xp, v, pull->bVirial && MASTER(cr), vir, dt, t);
+}
+
+static void make_local_pull_group(gmx_ga2la_t ga2la,
+ t_pull_group *pg, int start, int end)
+{
+ int i, ii;
+
+ pg->nat_loc = 0;
+ for (i = 0; i < pg->nat; i++)
+ {
+ ii = pg->ind[i];
+ if (ga2la)
+ {
+ if (!ga2la_get_home(ga2la, ii, &ii))
+ {
+ ii = -1;
+ }
+ }
+ if (ii >= start && ii < end)
+ {
+ /* This is a home atom, add it to the local pull group */
+ if (pg->nat_loc >= pg->nalloc_loc)
+ {
+ pg->nalloc_loc = over_alloc_dd(pg->nat_loc+1);
+ srenew(pg->ind_loc, pg->nalloc_loc);
+ if (pg->epgrppbc == epgrppbcCOS || pg->weight)
+ {
+ srenew(pg->weight_loc, pg->nalloc_loc);
+ }
+ }
+ pg->ind_loc[pg->nat_loc] = ii;
+ if (pg->weight)
+ {
+ pg->weight_loc[pg->nat_loc] = pg->weight[i];
+ }
+ pg->nat_loc++;
+ }
+ }
+}
+
+void dd_make_local_pull_groups(gmx_domdec_t *dd, t_pull *pull, t_mdatoms *md)
+{
+ gmx_ga2la_t ga2la;
+ int g;
+
+ if (dd)
+ {
+ ga2la = dd->ga2la;
+ }
+ else
+ {
+ ga2la = NULL;
+ }
+
+ for (g = 0; g < pull->ngroup; g++)
+ {
+ make_local_pull_group(ga2la, &pull->group[g],
+ 0, md->homenr);
+ }
+}
+
+static void init_pull_group_index(FILE *fplog, t_commrec *cr,
+ int g, t_pull_group *pg, ivec pulldims,
+ gmx_mtop_t *mtop, t_inputrec *ir, real lambda)
+{
+ int i, ii, d, nfrozen, ndim;
+ real m, w, mbd;
+ double tmass, wmass, wwmass;
+ gmx_groups_t *groups;
+ gmx_mtop_atomlookup_t alook;
+ t_atom *atom;
+
+ if (EI_ENERGY_MINIMIZATION(ir->eI) || ir->eI == eiBD)
+ {
+ /* There are no masses in the integrator.
+ * But we still want to have the correct mass-weighted COMs.
+ * So we store the real masses in the weights.
+ * We do not set nweight, so these weights do not end up in the tpx file.
+ */
+ if (pg->nweight == 0)
+ {
+ snew(pg->weight, pg->nat);
+ }
+ }
+
+ if (cr && PAR(cr))
+ {
+ pg->nat_loc = 0;
+ pg->nalloc_loc = 0;
+ pg->ind_loc = NULL;
+ pg->weight_loc = NULL;
+ }
+ else
+ {
+ pg->nat_loc = pg->nat;
+ pg->ind_loc = pg->ind;
+ if (pg->epgrppbc == epgrppbcCOS)
+ {
+ snew(pg->weight_loc, pg->nat);
+ }
+ else
+ {
+ pg->weight_loc = pg->weight;
+ }
+ }
+
+ groups = &mtop->groups;
+
+ alook = gmx_mtop_atomlookup_init(mtop);
+
+ nfrozen = 0;
+ tmass = 0;
+ wmass = 0;
+ wwmass = 0;
+ for (i = 0; i < pg->nat; i++)
+ {
+ ii = pg->ind[i];
+ gmx_mtop_atomnr_to_atom(alook, ii, &atom);
+ if (ir->opts.nFreeze)
+ {
+ for (d = 0; d < DIM; d++)
+ {
+ if (pulldims[d] && ir->opts.nFreeze[ggrpnr(groups, egcFREEZE, ii)][d])
+ {
+ nfrozen++;
+ }
+ }
+ }
+ if (ir->efep == efepNO)
+ {
+ m = atom->m;
+ }
+ else
+ {
+ m = (1 - lambda)*atom->m + lambda*atom->mB;
+ }
+ if (pg->nweight > 0)
+ {
+ w = pg->weight[i];
+ }
+ else
+ {
+ w = 1;
+ }
+ if (EI_ENERGY_MINIMIZATION(ir->eI))
+ {
+ /* Move the mass to the weight */
+ w *= m;
+ m = 1;
+ pg->weight[i] = w;
+ }
+ else if (ir->eI == eiBD)
+ {
+ if (ir->bd_fric)
+ {
+ mbd = ir->bd_fric*ir->delta_t;
+ }
+ else
+ {
+ if (groups->grpnr[egcTC] == NULL)
+ {
+ mbd = ir->delta_t/ir->opts.tau_t[0];
+ }
+ else
+ {
+ mbd = ir->delta_t/ir->opts.tau_t[groups->grpnr[egcTC][ii]];
+ }
+ }
+ w *= m/mbd;
+ m = mbd;
+ pg->weight[i] = w;
+ }
+ tmass += m;
+ wmass += m*w;
+ wwmass += m*w*w;
+ }
+
+ gmx_mtop_atomlookup_destroy(alook);
+
+ if (wmass == 0)
+ {
+ gmx_fatal(FARGS, "The total%s mass of pull group %d is zero",
+ pg->weight ? " weighted" : "", g);
+ }
+ if (fplog)
+ {
+ fprintf(fplog,
+ "Pull group %d: %5d atoms, mass %9.3f", g, pg->nat, tmass);
+ if (pg->weight || EI_ENERGY_MINIMIZATION(ir->eI) || ir->eI == eiBD)
+ {
+ fprintf(fplog, ", weighted mass %9.3f", wmass*wmass/wwmass);
+ }
+ if (pg->epgrppbc == epgrppbcCOS)
+ {
+ fprintf(fplog, ", cosine weighting will be used");
+ }
+ fprintf(fplog, "\n");
+ }
+
+ if (nfrozen == 0)
+ {
+ /* A value > 0 signals not frozen, it is updated later */
+ pg->invtm = 1.0;
+ }
+ else
+ {
+ ndim = 0;
+ for (d = 0; d < DIM; d++)
+ {
+ ndim += pulldims[d]*pg->nat;
+ }
+ if (fplog && nfrozen > 0 && nfrozen < ndim)
+ {
+ fprintf(fplog,
+ "\nWARNING: In pull group %d some, but not all of the degrees of freedom\n"
+ " that are subject to pulling are frozen.\n"
+ " For pulling the whole group will be frozen.\n\n",
+ g);
+ }
+ pg->invtm = 0.0;
+ pg->wscale = 1.0;
+ }
+}
+
+void init_pull(FILE *fplog, t_inputrec *ir, int nfile, const t_filenm fnm[],
+ gmx_mtop_t *mtop, t_commrec *cr, const output_env_t oenv, real lambda,
+ gmx_bool bOutFile, unsigned long Flags)
+{
+ t_pull *pull;
+ t_pull_group *pgrp;
+ int c, g, start = 0, end = 0, m;
+
+ pull = ir->pull;
+
+ pull->ePBC = ir->ePBC;
+ switch (pull->ePBC)
+ {
+ case epbcNONE: pull->npbcdim = 0; break;
+ case epbcXY: pull->npbcdim = 2; break;
+ default: pull->npbcdim = 3; break;
+ }
+
+ if (fplog)
+ {
+ gmx_bool bAbs, bCos;
+
+ bAbs = FALSE;
+ for (c = 0; c < pull->ncoord; c++)
+ {
+ if (pull->group[pull->coord[c].group[0]].nat == 0 ||
+ pull->group[pull->coord[c].group[1]].nat == 0)
+ {
+ bAbs = TRUE;
+ }
+ }
+
+ fprintf(fplog, "\nWill apply %s COM pulling in geometry '%s'\n",
+ EPULLTYPE(ir->ePull), EPULLGEOM(pull->eGeom));
+ fprintf(fplog, "with %d pull coordinate%s and %d group%s\n",
+ pull->ncoord, pull->ncoord == 1 ? "" : "s",
+ pull->ngroup, pull->ngroup == 1 ? "" : "s");
+ if (bAbs)
+ {
+ fprintf(fplog, "with an absolute reference\n");
+ }
+ bCos = FALSE;
+ for (g = 0; g < pull->ngroup; g++)
+ {
+ if (pull->group[g].nat > 1 &&
+ pull->group[g].pbcatom < 0)
+ {
+ /* We are using cosine weighting */
+ fprintf(fplog, "Cosine weighting is used for group %d\n", g);
+ bCos = TRUE;
+ }
+ }
+ if (bCos)
+ {
+ please_cite(fplog, "Engin2010");
+ }
+ }
+
+ /* We always add the virial contribution,
+ * except for geometry = direction_periodic where this is impossible.
+ */
+ pull->bVirial = (pull->eGeom != epullgDIRPBC);
+ if (getenv("GMX_NO_PULLVIR") != NULL)
+ {
+ if (fplog)
+ {
+ fprintf(fplog, "Found env. var., will not add the virial contribution of the COM pull forces\n");
+ }
+ pull->bVirial = FALSE;
+ }
+
+ pull->rbuf = NULL;
+ pull->dbuf = NULL;
+ pull->dbuf_cyl = NULL;
+ pull->bRefAt = FALSE;
+ pull->cosdim = -1;
+ for (g = 0; g < pull->ngroup; g++)
+ {
+ pgrp = &pull->group[g];
+ pgrp->epgrppbc = epgrppbcNONE;
+ if (pgrp->nat > 0)
+ {
+ /* Determine if we need to take PBC into account for calculating
+ * the COM's of the pull groups.
+ */
+ for (m = 0; m < pull->npbcdim; m++)
+ {
+ if (pull->dim[m] && pgrp->nat > 1)
+ {
+ if (pgrp->pbcatom >= 0)
+ {
+ pgrp->epgrppbc = epgrppbcREFAT;
+ pull->bRefAt = TRUE;
+ }
+ else
+ {
+ if (pgrp->weight)
+ {
+ gmx_fatal(FARGS, "Pull groups can not have relative weights and cosine weighting at same time");
+ }
+ pgrp->epgrppbc = epgrppbcCOS;
+ if (pull->cosdim >= 0 && pull->cosdim != m)
+ {
+ gmx_fatal(FARGS, "Can only use cosine weighting with pulling in one dimension (use mdp option pull_dim)");
+ }
+ pull->cosdim = m;
+ }
+ }
+ }
+ /* Set the indices */
+ init_pull_group_index(fplog, cr, g, pgrp, pull->dim, mtop, ir, lambda);
+ if (PULL_CYL(pull) && pgrp->invtm == 0)
+ {
+ gmx_fatal(FARGS, "Can not have frozen atoms in a cylinder pull group");
+ }
+ }
+ else
+ {
+ /* Absolute reference, set the inverse mass to zero */
+ pgrp->invtm = 0;
+ pgrp->wscale = 1;
+ }
+ }
+
+ /* if we use dynamic reference groups, do some initialising for them */
+ if (PULL_CYL(pull))
+ {
+ if (ir->ePull == epullCONSTRAINT && pull->ncoord > 1)
+ {
+ /* We can't easily update the single reference group with multiple
+ * constraints. This would require recalculating COMs.
+ */
+ gmx_fatal(FARGS, "Constraint COM pulling supports only one coordinate with geometry=cylinder, you can use umbrella pulling with multiple coordinates");
+ }
+
+ for (c = 0; c < pull->ncoord; c++)
+ {
+ if (pull->group[pull->coord[c].group[0]].nat == 0)
+ {
+ gmx_fatal(FARGS, "Dynamic reference groups are not supported when using absolute reference!\n");
+ }
+ }
+
+ snew(pull->dyna, pull->ncoord);
+ }
+
+ /* Only do I/O when we are doing dynamics and if we are the MASTER */
+ pull->out_x = NULL;
+ pull->out_f = NULL;
+ if (bOutFile)
+ {
+ if (pull->nstxout > 0)
+ {
+ pull->out_x = open_pull_out(opt2fn("-px", nfile, fnm), pull, oenv, TRUE, Flags);
+ }
+ if (pull->nstfout > 0)
+ {
+ pull->out_f = open_pull_out(opt2fn("-pf", nfile, fnm), pull, oenv,
+ FALSE, Flags);
+ }
+ }
+}
+
+void finish_pull(t_pull *pull)
+{
+ if (pull->out_x)
+ {
+ gmx_fio_fclose(pull->out_x);
+ }
+ if (pull->out_f)
+ {
+ gmx_fio_fclose(pull->out_f);
+ }
+}
--- /dev/null
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
+ * Copyright (c) 2001-2004, The GROMACS development team.
+ * Copyright (c) 2011,2012,2013,2014, by the GROMACS development team, led by
+ * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+ * and including many others, as listed in the AUTHORS file in the
+ * top-level source directory and at http://www.gromacs.org.
+ *
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
+ * of the License, or (at your option) any later version.
+ *
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+ *
+ * If you want to redistribute modifications to GROMACS, please
+ * consider that scientific software is very special. Version
+ * control is crucial - bugs must be traceable. We will be happy to
+ * consider code for inclusion in the official distribution, but
+ * derived work must not be called official GROMACS. Details are found
+ * in the README & COPYING files - if they are missing, get the
+ * official version at http://www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the research papers on the package. Check out http://www.gromacs.org.
+ */
+#ifdef HAVE_CONFIG_H
+#include <config.h>
+#endif
+
+#include "typedefs.h"
+#include "gromacs/utility/smalloc.h"
+#include "sysstuff.h"
+#include "vec.h"
+#include "vcm.h"
+#include "mdebin.h"
+#include "nrnb.h"
+#include "calcmu.h"
+#include "index.h"
+#include "vsite.h"
+#include "update.h"
+#include "ns.h"
+#include "mdrun.h"
+#include "md_support.h"
+#include "md_logging.h"
+#include "network.h"
+#include "xvgr.h"
+#include "physics.h"
+#include "names.h"
+#include "force.h"
+#include "disre.h"
+#include "orires.h"
+#include "pme.h"
+#include "mdatoms.h"
+#include "repl_ex.h"
+#include "deform.h"
+#include "qmmm.h"
+#include "domdec.h"
+#include "domdec_network.h"
+#include "gromacs/gmxlib/topsort.h"
+#include "coulomb.h"
+#include "constr.h"
+#include "shellfc.h"
+#include "gromacs/gmxpreprocess/compute_io.h"
+#include "checkpoint.h"
+#include "mtop_util.h"
+#include "sighandler.h"
+#include "txtdump.h"
+#include "gromacs/utility/cstringutil.h"
+#include "pme_loadbal.h"
+#include "bondf.h"
+#include "membed.h"
+#include "types/nlistheuristics.h"
+#include "types/iteratedconstraints.h"
+#include "nbnxn_cuda_data_mgmt.h"
+
+#include "gromacs/utility/gmxmpi.h"
+#include "gromacs/fileio/confio.h"
+#include "gromacs/fileio/trajectory_writing.h"
+#include "gromacs/fileio/trnio.h"
+#include "gromacs/fileio/trxio.h"
+#include "gromacs/fileio/xtcio.h"
+#include "gromacs/timing/wallcycle.h"
+#include "gromacs/timing/walltime_accounting.h"
+#include "gromacs/pulling/pull.h"
+#include "gromacs/swap/swapcoords.h"
+#include "gromacs/imd/imd.h"
+
+#ifdef GMX_FAHCORE
+#include "corewrap.h"
+#endif
+
+static void reset_all_counters(FILE *fplog, t_commrec *cr,
+ gmx_int64_t step,
+ gmx_int64_t *step_rel, t_inputrec *ir,
+ gmx_wallcycle_t wcycle, t_nrnb *nrnb,
+ gmx_walltime_accounting_t walltime_accounting,
+ nbnxn_cuda_ptr_t cu_nbv)
+{
+ char sbuf[STEPSTRSIZE];
+
+ /* Reset all the counters related to performance over the run */
+ md_print_warn(cr, fplog, "step %s: resetting all time and cycle counters\n",
+ gmx_step_str(step, sbuf));
+
+ if (cu_nbv)
+ {
+ nbnxn_cuda_reset_timings(cu_nbv);
+ }
+
+ wallcycle_stop(wcycle, ewcRUN);
+ wallcycle_reset_all(wcycle);
+ if (DOMAINDECOMP(cr))
+ {
+ reset_dd_statistics_counters(cr->dd);
+ }
+ init_nrnb(nrnb);
+ ir->init_step += *step_rel;
+ ir->nsteps -= *step_rel;
+ *step_rel = 0;
+ wallcycle_start(wcycle, ewcRUN);
+ walltime_accounting_start(walltime_accounting);
+ print_date_and_time(fplog, cr->nodeid, "Restarted time", gmx_gettime());
+}
+
+double do_md(FILE *fplog, t_commrec *cr, int nfile, const t_filenm fnm[],
+ const output_env_t oenv, gmx_bool bVerbose, gmx_bool bCompact,
+ int nstglobalcomm,
+ gmx_vsite_t *vsite, gmx_constr_t constr,
+ int stepout, t_inputrec *ir,
+ gmx_mtop_t *top_global,
+ t_fcdata *fcd,
+ t_state *state_global,
+ t_mdatoms *mdatoms,
+ t_nrnb *nrnb, gmx_wallcycle_t wcycle,
+ gmx_edsam_t ed, t_forcerec *fr,
+ int repl_ex_nst, int repl_ex_nex, int repl_ex_seed, gmx_membed_t membed,
+ real cpt_period, real max_hours,
+ const char gmx_unused *deviceOptions,
+ int imdport,
+ unsigned long Flags,
+ gmx_walltime_accounting_t walltime_accounting)
+{
+ gmx_mdoutf_t outf = NULL;
+ gmx_int64_t step, step_rel;
+ double elapsed_time;
+ double t, t0, lam0[efptNR];
+ gmx_bool bGStatEveryStep, bGStat, bCalcVir, bCalcEner;
+ gmx_bool bNS, bNStList, bSimAnn, bStopCM, bRerunMD, bNotLastFrame = FALSE,
+ bFirstStep, bStateFromCP, bStateFromTPX, bInitStep, bLastStep,
+ bBornRadii, bStartingFromCpt;
+ gmx_bool bDoDHDL = FALSE, bDoFEP = FALSE, bDoExpanded = FALSE;
+ gmx_bool do_ene, do_log, do_verbose, bRerunWarnNoV = TRUE,
+ bForceUpdate = FALSE, bCPT;
+ gmx_bool bMasterState;
+ int force_flags, cglo_flags;
+ tensor force_vir, shake_vir, total_vir, tmp_vir, pres;
+ int i, m;
+ t_trxstatus *status;
+ rvec mu_tot;
+ t_vcm *vcm;
+ t_state *bufstate = NULL;
+ matrix *scale_tot, pcoupl_mu, M, ebox;
+ gmx_nlheur_t nlh;
+ t_trxframe rerun_fr;
+ gmx_repl_ex_t repl_ex = NULL;
+ int nchkpt = 1;
+ gmx_localtop_t *top;
+ t_mdebin *mdebin = NULL;
+ t_state *state = NULL;
+ rvec *f_global = NULL;
+ gmx_enerdata_t *enerd;
+ rvec *f = NULL;
+ gmx_global_stat_t gstat;
+ gmx_update_t upd = NULL;
+ t_graph *graph = NULL;
+ globsig_t gs;
+ gmx_groups_t *groups;
+ gmx_ekindata_t *ekind, *ekind_save;
+ gmx_shellfc_t shellfc;
+ int count, nconverged = 0;
+ real timestep = 0;
+ double tcount = 0;
+ gmx_bool bConverged = TRUE, bOK, bSumEkinhOld, bExchanged, bNeedRepartition;
+ gmx_bool bAppend;
+ gmx_bool bResetCountersHalfMaxH = FALSE;
+ gmx_bool bVV, bIterativeCase, bFirstIterate, bTemp, bPres, bTrotter;
+ gmx_bool bUpdateDoLR;
+ real dvdl_constr;
+ rvec *cbuf = NULL;
+ matrix lastbox;
+ real veta_save, scalevir, tracevir;
+ real vetanew = 0;
+ int lamnew = 0;
+ /* for FEP */
+ int nstfep;
+ double cycles;
+ real saved_conserved_quantity = 0;
+ real last_ekin = 0;
+ int iter_i;
+ t_extmass MassQ;
+ int **trotter_seq;
+ char sbuf[STEPSTRSIZE], sbuf2[STEPSTRSIZE];
+ int handled_stop_condition = gmx_stop_cond_none; /* compare to get_stop_condition*/
+ gmx_iterate_t iterate;
+ gmx_int64_t multisim_nsteps = -1; /* number of steps to do before first multisim
+ simulation stops. If equal to zero, don't
+ communicate any more between multisims.*/
+ /* PME load balancing data for GPU kernels */
+ pme_load_balancing_t pme_loadbal = NULL;
+ double cycles_pmes;
+ gmx_bool bPMETuneTry = FALSE, bPMETuneRunning = FALSE;
+
+ /* Interactive MD */
+ gmx_bool bIMDstep = FALSE;
+
+#ifdef GMX_FAHCORE
+ /* Temporary addition for FAHCORE checkpointing */
+ int chkpt_ret;
+#endif
+
+ /* Check for special mdrun options */
+ bRerunMD = (Flags & MD_RERUN);
+ bAppend = (Flags & MD_APPENDFILES);
+ if (Flags & MD_RESETCOUNTERSHALFWAY)
+ {
+ if (ir->nsteps > 0)
+ {
+ /* Signal to reset the counters half the simulation steps. */
+ wcycle_set_reset_counters(wcycle, ir->nsteps/2);
+ }
+ /* Signal to reset the counters halfway the simulation time. */
+ bResetCountersHalfMaxH = (max_hours > 0);
+ }
+
+ /* md-vv uses averaged full step velocities for T-control
+ md-vv-avek uses averaged half step velocities for T-control (but full step ekin for P control)
+ md uses averaged half step kinetic energies to determine temperature unless defined otherwise by GMX_EKIN_AVE_VEL; */
+ bVV = EI_VV(ir->eI);
+ if (bVV) /* to store the initial velocities while computing virial */
+ {
+ snew(cbuf, top_global->natoms);
+ }
+ /* all the iteratative cases - only if there are constraints */
+ bIterativeCase = ((IR_NPH_TROTTER(ir) || IR_NPT_TROTTER(ir)) && (constr) && (!bRerunMD));
+ gmx_iterate_init(&iterate, FALSE); /* The default value of iterate->bIterationActive is set to
+ false in this step. The correct value, true or false,
+ is set at each step, as it depends on the frequency of temperature
+ and pressure control.*/
+ bTrotter = (bVV && (IR_NPT_TROTTER(ir) || IR_NPH_TROTTER(ir) || IR_NVT_TROTTER(ir)));
+
+ if (bRerunMD)
+ {
+ /* Since we don't know if the frames read are related in any way,
+ * rebuild the neighborlist at every step.
+ */
+ ir->nstlist = 1;
+ ir->nstcalcenergy = 1;
+ nstglobalcomm = 1;
+ }
+
+ check_ir_old_tpx_versions(cr, fplog, ir, top_global);
+
+ nstglobalcomm = check_nstglobalcomm(fplog, cr, nstglobalcomm, ir);
+ bGStatEveryStep = (nstglobalcomm == 1);
+
+ if (!bGStatEveryStep && ir->nstlist == -1 && fplog != NULL)
+ {
+ fprintf(fplog,
+ "To reduce the energy communication with nstlist = -1\n"
+ "the neighbor list validity should not be checked at every step,\n"
+ "this means that exact integration is not guaranteed.\n"
+ "The neighbor list validity is checked after:\n"
+ " <n.list life time> - 2*std.dev.(n.list life time) steps.\n"
+ "In most cases this will result in exact integration.\n"
+ "This reduces the energy communication by a factor of 2 to 3.\n"
+ "If you want less energy communication, set nstlist > 3.\n\n");
+ }
+
+ if (bRerunMD)
+ {
+ ir->nstxout_compressed = 0;
+ }
+ groups = &top_global->groups;
+
+ /* Initial values */
+ init_md(fplog, cr, ir, oenv, &t, &t0, state_global->lambda,
+ &(state_global->fep_state), lam0,
+ nrnb, top_global, &upd,
+ nfile, fnm, &outf, &mdebin,
+ force_vir, shake_vir, mu_tot, &bSimAnn, &vcm, Flags);
+
+ clear_mat(total_vir);
+ clear_mat(pres);
+ /* Energy terms and groups */
+ snew(enerd, 1);
+ init_enerdata(top_global->groups.grps[egcENER].nr, ir->fepvals->n_lambda,
+ enerd);
+ if (DOMAINDECOMP(cr))
+ {
+ f = NULL;
+ }
+ else
+ {
+ snew(f, top_global->natoms);
+ }
+
+ /* Kinetic energy data */
+ snew(ekind, 1);
+ init_ekindata(fplog, top_global, &(ir->opts), ekind);
+ /* needed for iteration of constraints */
+ snew(ekind_save, 1);
+ init_ekindata(fplog, top_global, &(ir->opts), ekind_save);
+ /* Copy the cos acceleration to the groups struct */
+ ekind->cosacc.cos_accel = ir->cos_accel;
+
+ gstat = global_stat_init(ir);
+ debug_gmx();
+
+ /* Check for polarizable models and flexible constraints */
+ shellfc = init_shell_flexcon(fplog, fr->cutoff_scheme == ecutsVERLET,
+ top_global, n_flexible_constraints(constr),
+ (ir->bContinuation ||
+ (DOMAINDECOMP(cr) && !MASTER(cr))) ?
+ NULL : state_global->x);
+
++ if (shellfc && ir->eI == eiNM)
++ {
++ /* Currently shells don't work with Normal Modes */
++ gmx_fatal(FARGS, "Normal Mode analysis is not supported with shells.\nIf you'd like to help with adding support, we have an open discussion at http://redmine.gromacs.org/issues/879\n");
++ }
++
++ if (vsite && ir->eI == eiNM)
++ {
++ /* Currently virtual sites don't work with Normal Modes */
++ gmx_fatal(FARGS, "Normal Mode analysis is not supported with virtual sites.\nIf you'd like to help with adding support, we have an open discussion at http://redmine.gromacs.org/issues/879\n");
++ }
++
+ if (DEFORM(*ir))
+ {
+ tMPI_Thread_mutex_lock(&deform_init_box_mutex);
+ set_deform_reference_box(upd,
+ deform_init_init_step_tpx,
+ deform_init_box_tpx);
+ tMPI_Thread_mutex_unlock(&deform_init_box_mutex);
+ }
+
+ {
+ double io = compute_io(ir, top_global->natoms, groups, mdebin->ebin->nener, 1);
+ if ((io > 2000) && MASTER(cr))
+ {
+ fprintf(stderr,
+ "\nWARNING: This run will generate roughly %.0f Mb of data\n\n",
+ io);
+ }
+ }
+
+ if (DOMAINDECOMP(cr))
+ {
+ top = dd_init_local_top(top_global);
+
+ snew(state, 1);
+ dd_init_local_state(cr->dd, state_global, state);
+
+ if (DDMASTER(cr->dd) && ir->nstfout)
+ {
+ snew(f_global, state_global->natoms);
+ }
+ }
+ else
+ {
+ top = gmx_mtop_generate_local_top(top_global, ir);
+
+ forcerec_set_excl_load(fr, top);
+
+ state = serial_init_local_state(state_global);
+ f_global = f;
+
+ atoms2md(top_global, ir, 0, NULL, top_global->natoms, mdatoms);
+
+ if (vsite)
+ {
+ set_vsite_top(vsite, top, mdatoms, cr);
+ }
+
+ if (ir->ePBC != epbcNONE && !fr->bMolPBC)
+ {
+ graph = mk_graph(fplog, &(top->idef), 0, top_global->natoms, FALSE, FALSE);
+ }
+
+ if (shellfc)
+ {
+ make_local_shells(cr, mdatoms, shellfc);
+ }
+
+ setup_bonded_threading(fr, &top->idef);
+ }
+
+ /* Set up interactive MD (IMD) */
+ init_IMD(ir, cr, top_global, fplog, ir->nstcalcenergy, state_global->x,
+ nfile, fnm, oenv, imdport, Flags);
+
+ if (DOMAINDECOMP(cr))
+ {
+ /* Distribute the charge groups over the nodes from the master node */
+ dd_partition_system(fplog, ir->init_step, cr, TRUE, 1,
+ state_global, top_global, ir,
+ state, &f, mdatoms, top, fr,
+ vsite, shellfc, constr,
+ nrnb, wcycle, FALSE);
+
+ }
+
+ update_mdatoms(mdatoms, state->lambda[efptMASS]);
+
+ if (opt2bSet("-cpi", nfile, fnm))
+ {
+ bStateFromCP = gmx_fexist_master(opt2fn_master("-cpi", nfile, fnm, cr), cr);
+ }
+ else
+ {
+ bStateFromCP = FALSE;
+ }
+
+ if (ir->bExpanded)
+ {
+ init_expanded_ensemble(bStateFromCP, ir, &state->dfhist);
+ }
+
+ if (MASTER(cr))
+ {
+ if (bStateFromCP)
+ {
+ /* Update mdebin with energy history if appending to output files */
+ if (Flags & MD_APPENDFILES)
+ {
+ restore_energyhistory_from_state(mdebin, &state_global->enerhist);
+ }
+ else
+ {
+ /* We might have read an energy history from checkpoint,
+ * free the allocated memory and reset the counts.
+ */
+ done_energyhistory(&state_global->enerhist);
+ init_energyhistory(&state_global->enerhist);
+ }
+ }
+ /* Set the initial energy history in state by updating once */
+ update_energyhistory(&state_global->enerhist, mdebin);
+ }
+
+ /* Initialize constraints */
+ if (constr && !DOMAINDECOMP(cr))
+ {
+ set_constraints(constr, top, ir, mdatoms, cr);
+ }
+
+ if (repl_ex_nst > 0)
+ {
+ /* We need to be sure replica exchange can only occur
+ * when the energies are current */
+ check_nst_param(fplog, cr, "nstcalcenergy", ir->nstcalcenergy,
+ "repl_ex_nst", &repl_ex_nst);
+ /* This check needs to happen before inter-simulation
+ * signals are initialized, too */
+ }
+ if (repl_ex_nst > 0 && MASTER(cr))
+ {
+ repl_ex = init_replica_exchange(fplog, cr->ms, state_global, ir,
+ repl_ex_nst, repl_ex_nex, repl_ex_seed);
+ }
+
+ /* PME tuning is only supported with GPUs or PME nodes and not with rerun.
+ * PME tuning is not supported with PME only for LJ and not for Coulomb.
+ */
+ if ((Flags & MD_TUNEPME) &&
+ EEL_PME(fr->eeltype) &&
+ ( (fr->cutoff_scheme == ecutsVERLET && fr->nbv->bUseGPU) || !(cr->duty & DUTY_PME)) &&
+ !bRerunMD)
+ {
+ pme_loadbal_init(&pme_loadbal, ir, state->box, fr->ic, fr->pmedata);
+ cycles_pmes = 0;
+ if (cr->duty & DUTY_PME)
+ {
+ /* Start tuning right away, as we can't measure the load */
+ bPMETuneRunning = TRUE;
+ }
+ else
+ {
+ /* Separate PME nodes, we can measure the PP/PME load balance */
+ bPMETuneTry = TRUE;
+ }
+ }
+
+ if (!ir->bContinuation && !bRerunMD)
+ {
+ if (mdatoms->cFREEZE && (state->flags & (1<<estV)))
+ {
+ /* Set the velocities of frozen particles to zero */
+ for (i = 0; i < mdatoms->homenr; i++)
+ {
+ for (m = 0; m < DIM; m++)
+ {
+ if (ir->opts.nFreeze[mdatoms->cFREEZE[i]][m])
+ {
+ state->v[i][m] = 0;
+ }
+ }
+ }
+ }
+
+ if (constr)
+ {
+ /* Constrain the initial coordinates and velocities */
+ do_constrain_first(fplog, constr, ir, mdatoms, state,
+ cr, nrnb, fr, top);
+ }
+ if (vsite)
+ {
+ /* Construct the virtual sites for the initial configuration */
+ construct_vsites(vsite, state->x, ir->delta_t, NULL,
+ top->idef.iparams, top->idef.il,
+ fr->ePBC, fr->bMolPBC, cr, state->box);
+ }
+ }
+
+ debug_gmx();
+
+ /* set free energy calculation frequency as the minimum
+ greatest common denominator of nstdhdl, nstexpanded, and repl_ex_nst*/
+ nstfep = ir->fepvals->nstdhdl;
+ if (ir->bExpanded)
+ {
+ nstfep = gmx_greatest_common_divisor(ir->fepvals->nstdhdl, nstfep);
+ }
+ if (repl_ex_nst > 0)
+ {
+ nstfep = gmx_greatest_common_divisor(repl_ex_nst, nstfep);
+ }
+
+ /* I'm assuming we need global communication the first time! MRS */
+ cglo_flags = (CGLO_TEMPERATURE | CGLO_GSTAT
+ | ((ir->comm_mode != ecmNO) ? CGLO_STOPCM : 0)
+ | (bVV ? CGLO_PRESSURE : 0)
+ | (bVV ? CGLO_CONSTRAINT : 0)
+ | (bRerunMD ? CGLO_RERUNMD : 0)
+ | ((Flags & MD_READ_EKIN) ? CGLO_READEKIN : 0));
+
+ bSumEkinhOld = FALSE;
+ compute_globals(fplog, gstat, cr, ir, fr, ekind, state, state_global, mdatoms, nrnb, vcm,
+ NULL, enerd, force_vir, shake_vir, total_vir, pres, mu_tot,
+ constr, NULL, FALSE, state->box,
+ top_global, &bSumEkinhOld, cglo_flags);
+ if (ir->eI == eiVVAK)
+ {
+ /* a second call to get the half step temperature initialized as well */
+ /* we do the same call as above, but turn the pressure off -- internally to
+ compute_globals, this is recognized as a velocity verlet half-step
+ kinetic energy calculation. This minimized excess variables, but
+ perhaps loses some logic?*/
+
+ compute_globals(fplog, gstat, cr, ir, fr, ekind, state, state_global, mdatoms, nrnb, vcm,
+ NULL, enerd, force_vir, shake_vir, total_vir, pres, mu_tot,
+ constr, NULL, FALSE, state->box,
+ top_global, &bSumEkinhOld,
+ cglo_flags &~(CGLO_STOPCM | CGLO_PRESSURE));
+ }
+
+ /* Calculate the initial half step temperature, and save the ekinh_old */
+ if (!(Flags & MD_STARTFROMCPT))
+ {
+ for (i = 0; (i < ir->opts.ngtc); i++)
+ {
+ copy_mat(ekind->tcstat[i].ekinh, ekind->tcstat[i].ekinh_old);
+ }
+ }
+ if (ir->eI != eiVV)
+ {
+ enerd->term[F_TEMP] *= 2; /* result of averages being done over previous and current step,
+ and there is no previous step */
+ }
+
+ /* if using an iterative algorithm, we need to create a working directory for the state. */
+ if (bIterativeCase)
+ {
+ bufstate = init_bufstate(state);
+ }
+
+ /* need to make an initiation call to get the Trotter variables set, as well as other constants for non-trotter
+ temperature control */
+ trotter_seq = init_npt_vars(ir, state, &MassQ, bTrotter);
+
+ if (MASTER(cr))
+ {
+ if (constr && !ir->bContinuation && ir->eConstrAlg == econtLINCS)
+ {
+ fprintf(fplog,
+ "RMS relative constraint deviation after constraining: %.2e\n",
+ constr_rmsd(constr, FALSE));
+ }
+ if (EI_STATE_VELOCITY(ir->eI))
+ {
+ fprintf(fplog, "Initial temperature: %g K\n", enerd->term[F_TEMP]);
+ }
+ if (bRerunMD)
+ {
+ fprintf(stderr, "starting md rerun '%s', reading coordinates from"
+ " input trajectory '%s'\n\n",
+ *(top_global->name), opt2fn("-rerun", nfile, fnm));
+ if (bVerbose)
+ {
+ fprintf(stderr, "Calculated time to finish depends on nsteps from "
+ "run input file,\nwhich may not correspond to the time "
+ "needed to process input trajectory.\n\n");
+ }
+ }
+ else
+ {
+ char tbuf[20];
+ fprintf(stderr, "starting mdrun '%s'\n",
+ *(top_global->name));
+ if (ir->nsteps >= 0)
+ {
+ sprintf(tbuf, "%8.1f", (ir->init_step+ir->nsteps)*ir->delta_t);
+ }
+ else
+ {
+ sprintf(tbuf, "%s", "infinite");
+ }
+ if (ir->init_step > 0)
+ {
+ fprintf(stderr, "%s steps, %s ps (continuing from step %s, %8.1f ps).\n",
+ gmx_step_str(ir->init_step+ir->nsteps, sbuf), tbuf,
+ gmx_step_str(ir->init_step, sbuf2),
+ ir->init_step*ir->delta_t);
+ }
+ else
+ {
+ fprintf(stderr, "%s steps, %s ps.\n",
+ gmx_step_str(ir->nsteps, sbuf), tbuf);
+ }
+ }
+ fprintf(fplog, "\n");
+ }
+
+ walltime_accounting_start(walltime_accounting);
+ wallcycle_start(wcycle, ewcRUN);
+ print_start(fplog, cr, walltime_accounting, "mdrun");
+
+ /* safest point to do file checkpointing is here. More general point would be immediately before integrator call */
+#ifdef GMX_FAHCORE
+ chkpt_ret = fcCheckPointParallel( cr->nodeid,
+ NULL, 0);
+ if (chkpt_ret == 0)
+ {
+ gmx_fatal( 3, __FILE__, __LINE__, "Checkpoint error on step %d\n", 0 );
+ }
+#endif
+
+ debug_gmx();
+ /***********************************************************
+ *
+ * Loop over MD steps
+ *
+ ************************************************************/
+
+ /* if rerunMD then read coordinates and velocities from input trajectory */
+ if (bRerunMD)
+ {
+ if (getenv("GMX_FORCE_UPDATE"))
+ {
+ bForceUpdate = TRUE;
+ }
+
+ rerun_fr.natoms = 0;
+ if (MASTER(cr))
+ {
+ bNotLastFrame = read_first_frame(oenv, &status,
+ opt2fn("-rerun", nfile, fnm),
+ &rerun_fr, TRX_NEED_X | TRX_READ_V);
+ if (rerun_fr.natoms != top_global->natoms)
+ {
+ gmx_fatal(FARGS,
+ "Number of atoms in trajectory (%d) does not match the "
+ "run input file (%d)\n",
+ rerun_fr.natoms, top_global->natoms);
+ }
+ if (ir->ePBC != epbcNONE)
+ {
+ if (!rerun_fr.bBox)
+ {
+ gmx_fatal(FARGS, "Rerun trajectory frame step %d time %f does not contain a box, while pbc is used", rerun_fr.step, rerun_fr.time);
+ }
+ if (max_cutoff2(ir->ePBC, rerun_fr.box) < sqr(fr->rlistlong))
+ {
+ gmx_fatal(FARGS, "Rerun trajectory frame step %d time %f has too small box dimensions", rerun_fr.step, rerun_fr.time);
+ }
+ }
+ }
+
+ if (PAR(cr))
+ {
+ rerun_parallel_comm(cr, &rerun_fr, &bNotLastFrame);
+ }
+
+ if (ir->ePBC != epbcNONE)
+ {
+ /* Set the shift vectors.
+ * Necessary here when have a static box different from the tpr box.
+ */
+ calc_shifts(rerun_fr.box, fr->shift_vec);
+ }
+ }
+
+ /* loop over MD steps or if rerunMD to end of input trajectory */
+ bFirstStep = TRUE;
+ /* Skip the first Nose-Hoover integration when we get the state from tpx */
+ bStateFromTPX = !bStateFromCP;
+ bInitStep = bFirstStep && (bStateFromTPX || bVV);
+ bStartingFromCpt = (Flags & MD_STARTFROMCPT) && bInitStep;
+ bLastStep = FALSE;
+ bSumEkinhOld = FALSE;
+ bExchanged = FALSE;
+ bNeedRepartition = FALSE;
+
+ init_global_signals(&gs, cr, ir, repl_ex_nst);
+
+ step = ir->init_step;
+ step_rel = 0;
+
+ if (ir->nstlist == -1)
+ {
+ init_nlistheuristics(&nlh, bGStatEveryStep, step);
+ }
+
+ if (MULTISIM(cr) && (repl_ex_nst <= 0 ))
+ {
+ /* check how many steps are left in other sims */
+ multisim_nsteps = get_multisim_nsteps(cr, ir->nsteps);
+ }
+
+
+ /* and stop now if we should */
+ bLastStep = (bRerunMD || (ir->nsteps >= 0 && step_rel > ir->nsteps) ||
+ ((multisim_nsteps >= 0) && (step_rel >= multisim_nsteps )));
+ while (!bLastStep || (bRerunMD && bNotLastFrame))
+ {
+
+ wallcycle_start(wcycle, ewcSTEP);
+
+ if (bRerunMD)
+ {
+ if (rerun_fr.bStep)
+ {
+ step = rerun_fr.step;
+ step_rel = step - ir->init_step;
+ }
+ if (rerun_fr.bTime)
+ {
+ t = rerun_fr.time;
+ }
+ else
+ {
+ t = step;
+ }
+ }
+ else
+ {
+ bLastStep = (step_rel == ir->nsteps);
+ t = t0 + step*ir->delta_t;
+ }
+
+ if (ir->efep != efepNO || ir->bSimTemp)
+ {
+ /* find and set the current lambdas. If rerunning, we either read in a state, or a lambda value,
+ requiring different logic. */
+
+ set_current_lambdas(step, ir->fepvals, bRerunMD, &rerun_fr, state_global, state, lam0);
+ bDoDHDL = do_per_step(step, ir->fepvals->nstdhdl);
+ bDoFEP = (do_per_step(step, nstfep) && (ir->efep != efepNO));
+ bDoExpanded = (do_per_step(step, ir->expandedvals->nstexpanded)
+ && (ir->bExpanded) && (step > 0) && (!bStartingFromCpt));
+ }
+
+ if (bSimAnn)
+ {
+ update_annealing_target_temp(&(ir->opts), t);
+ }
+
+ if (bRerunMD)
+ {
+ if (!DOMAINDECOMP(cr) || MASTER(cr))
+ {
+ for (i = 0; i < state_global->natoms; i++)
+ {
+ copy_rvec(rerun_fr.x[i], state_global->x[i]);
+ }
+ if (rerun_fr.bV)
+ {
+ for (i = 0; i < state_global->natoms; i++)
+ {
+ copy_rvec(rerun_fr.v[i], state_global->v[i]);
+ }
+ }
+ else
+ {
+ for (i = 0; i < state_global->natoms; i++)
+ {
+ clear_rvec(state_global->v[i]);
+ }
+ if (bRerunWarnNoV)
+ {
+ fprintf(stderr, "\nWARNING: Some frames do not contain velocities.\n"
+ " Ekin, temperature and pressure are incorrect,\n"
+ " the virial will be incorrect when constraints are present.\n"
+ "\n");
+ bRerunWarnNoV = FALSE;
+ }
+ }
+ }
+ copy_mat(rerun_fr.box, state_global->box);
+ copy_mat(state_global->box, state->box);
+
+ if (vsite && (Flags & MD_RERUN_VSITE))
+ {
+ if (DOMAINDECOMP(cr))
+ {
+ gmx_fatal(FARGS, "Vsite recalculation with -rerun is not implemented with domain decomposition, use a single rank");
+ }
+ if (graph)
+ {
+ /* Following is necessary because the graph may get out of sync
+ * with the coordinates if we only have every N'th coordinate set
+ */
+ mk_mshift(fplog, graph, fr->ePBC, state->box, state->x);
+ shift_self(graph, state->box, state->x);
+ }
+ construct_vsites(vsite, state->x, ir->delta_t, state->v,
+ top->idef.iparams, top->idef.il,
+ fr->ePBC, fr->bMolPBC, cr, state->box);
+ if (graph)
+ {
+ unshift_self(graph, state->box, state->x);
+ }
+ }
+ }
+
+ /* Stop Center of Mass motion */
+ bStopCM = (ir->comm_mode != ecmNO && do_per_step(step, ir->nstcomm));
+
+ if (bRerunMD)
+ {
+ /* for rerun MD always do Neighbour Searching */
+ bNS = (bFirstStep || ir->nstlist != 0);
+ bNStList = bNS;
+ }
+ else
+ {
+ /* Determine whether or not to do Neighbour Searching and LR */
+ bNStList = (ir->nstlist > 0 && step % ir->nstlist == 0);
+
+ bNS = (bFirstStep || bExchanged || bNeedRepartition || bNStList || bDoFEP ||
+ (ir->nstlist == -1 && nlh.nabnsb > 0));
+
+ if (bNS && ir->nstlist == -1)
+ {
+ set_nlistheuristics(&nlh, bFirstStep || bExchanged || bNeedRepartition || bDoFEP, step);
+ }
+ }
+
+ /* check whether we should stop because another simulation has
+ stopped. */
+ if (MULTISIM(cr))
+ {
+ if ( (multisim_nsteps >= 0) && (step_rel >= multisim_nsteps) &&
+ (multisim_nsteps != ir->nsteps) )
+ {
+ if (bNS)
+ {
+ if (MASTER(cr))
+ {
+ fprintf(stderr,
+ "Stopping simulation %d because another one has finished\n",
+ cr->ms->sim);
+ }
+ bLastStep = TRUE;
+ gs.sig[eglsCHKPT] = 1;
+ }
+ }
+ }
+
+ /* < 0 means stop at next step, > 0 means stop at next NS step */
+ if ( (gs.set[eglsSTOPCOND] < 0) ||
+ ( (gs.set[eglsSTOPCOND] > 0) && (bNStList || ir->nstlist == 0) ) )
+ {
+ bLastStep = TRUE;
+ }
+
+ /* Determine whether or not to update the Born radii if doing GB */
+ bBornRadii = bFirstStep;
+ if (ir->implicit_solvent && (step % ir->nstgbradii == 0))
+ {
+ bBornRadii = TRUE;
+ }
+
+ do_log = do_per_step(step, ir->nstlog) || bFirstStep || bLastStep;
+ do_verbose = bVerbose &&
+ (step % stepout == 0 || bFirstStep || bLastStep);
+
+ if (bNS && !(bFirstStep && ir->bContinuation && !bRerunMD))
+ {
+ if (bRerunMD)
+ {
+ bMasterState = TRUE;
+ }
+ else
+ {
+ bMasterState = FALSE;
+ /* Correct the new box if it is too skewed */
+ if (DYNAMIC_BOX(*ir))
+ {
+ if (correct_box(fplog, step, state->box, graph))
+ {
+ bMasterState = TRUE;
+ }
+ }
+ if (DOMAINDECOMP(cr) && bMasterState)
+ {
+ dd_collect_state(cr->dd, state, state_global);
+ }
+ }
+
+ if (DOMAINDECOMP(cr))
+ {
+ /* Repartition the domain decomposition */
+ wallcycle_start(wcycle, ewcDOMDEC);
+ dd_partition_system(fplog, step, cr,
+ bMasterState, nstglobalcomm,
+ state_global, top_global, ir,
+ state, &f, mdatoms, top, fr,
+ vsite, shellfc, constr,
+ nrnb, wcycle,
+ do_verbose && !bPMETuneRunning);
+ wallcycle_stop(wcycle, ewcDOMDEC);
+ /* If using an iterative integrator, reallocate space to match the decomposition */
+ }
+ }
+
+ if (MASTER(cr) && do_log)
+ {
+ print_ebin_header(fplog, step, t, state->lambda[efptFEP]); /* can we improve the information printed here? */
+ }
+
+ if (ir->efep != efepNO)
+ {
+ update_mdatoms(mdatoms, state->lambda[efptMASS]);
+ }
+
+ if ((bRerunMD && rerun_fr.bV) || bExchanged)
+ {
+
+ /* We need the kinetic energy at minus the half step for determining
+ * the full step kinetic energy and possibly for T-coupling.*/
+ /* This may not be quite working correctly yet . . . . */
+ compute_globals(fplog, gstat, cr, ir, fr, ekind, state, state_global, mdatoms, nrnb, vcm,
+ wcycle, enerd, NULL, NULL, NULL, NULL, mu_tot,
+ constr, NULL, FALSE, state->box,
+ top_global, &bSumEkinhOld,
+ CGLO_RERUNMD | CGLO_GSTAT | CGLO_TEMPERATURE);
+ }
+ clear_mat(force_vir);
+
+ /* We write a checkpoint at this MD step when:
+ * either at an NS step when we signalled through gs,
+ * or at the last step (but not when we do not want confout),
+ * but never at the first step or with rerun.
+ */
+ bCPT = (((gs.set[eglsCHKPT] && (bNS || ir->nstlist == 0)) ||
+ (bLastStep && (Flags & MD_CONFOUT))) &&
+ step > ir->init_step && !bRerunMD);
+ if (bCPT)
+ {
+ gs.set[eglsCHKPT] = 0;
+ }
+
+ /* Determine the energy and pressure:
+ * at nstcalcenergy steps and at energy output steps (set below).
+ */
+ if (EI_VV(ir->eI) && (!bInitStep))
+ {
+ /* for vv, the first half of the integration actually corresponds
+ to the previous step. bCalcEner is only required to be evaluated on the 'next' step,
+ but the virial needs to be calculated on both the current step and the 'next' step. Future
+ reorganization may be able to get rid of one of the bCalcVir=TRUE steps. */
+
+ bCalcEner = do_per_step(step-1, ir->nstcalcenergy);
+ bCalcVir = bCalcEner ||
+ (ir->epc != epcNO && (do_per_step(step, ir->nstpcouple) || do_per_step(step-1, ir->nstpcouple)));
+ }
+ else
+ {
+ bCalcEner = do_per_step(step, ir->nstcalcenergy);
+ bCalcVir = bCalcEner ||
+ (ir->epc != epcNO && do_per_step(step, ir->nstpcouple));
+ }
+
+ /* Do we need global communication ? */
+ bGStat = (bCalcVir || bCalcEner || bStopCM ||
+ do_per_step(step, nstglobalcomm) || (bVV && IR_NVT_TROTTER(ir) && do_per_step(step-1, nstglobalcomm)) ||
+ (ir->nstlist == -1 && !bRerunMD && step >= nlh.step_nscheck));
+
+ do_ene = (do_per_step(step, ir->nstenergy) || bLastStep);
+
+ if (do_ene || do_log)
+ {
+ bCalcVir = TRUE;
+ bCalcEner = TRUE;
+ bGStat = TRUE;
+ }
+
+ /* these CGLO_ options remain the same throughout the iteration */
+ cglo_flags = ((bRerunMD ? CGLO_RERUNMD : 0) |
+ (bGStat ? CGLO_GSTAT : 0)
+ );
+
+ force_flags = (GMX_FORCE_STATECHANGED |
+ ((DYNAMIC_BOX(*ir) || bRerunMD) ? GMX_FORCE_DYNAMICBOX : 0) |
+ GMX_FORCE_ALLFORCES |
+ GMX_FORCE_SEPLRF |
+ (bCalcVir ? GMX_FORCE_VIRIAL : 0) |
+ (bCalcEner ? GMX_FORCE_ENERGY : 0) |
+ (bDoFEP ? GMX_FORCE_DHDL : 0)
+ );
+
+ if (fr->bTwinRange)
+ {
+ if (do_per_step(step, ir->nstcalclr))
+ {
+ force_flags |= GMX_FORCE_DO_LR;
+ }
+ }
+
+ if (shellfc)
+ {
+ /* Now is the time to relax the shells */
+ count = relax_shell_flexcon(fplog, cr, bVerbose, step,
+ ir, bNS, force_flags,
+ top,
+ constr, enerd, fcd,
+ state, f, force_vir, mdatoms,
+ nrnb, wcycle, graph, groups,
+ shellfc, fr, bBornRadii, t, mu_tot,
+ &bConverged, vsite,
+ mdoutf_get_fp_field(outf));
+ tcount += count;
+
+ if (bConverged)
+ {
+ nconverged++;
+ }
+ }
+ else
+ {
+ /* The coordinates (x) are shifted (to get whole molecules)
+ * in do_force.
+ * This is parallellized as well, and does communication too.
+ * Check comments in sim_util.c
+ */
+ do_force(fplog, cr, ir, step, nrnb, wcycle, top, groups,
+ state->box, state->x, &state->hist,
+ f, force_vir, mdatoms, enerd, fcd,
+ state->lambda, graph,
+ fr, vsite, mu_tot, t, mdoutf_get_fp_field(outf), ed, bBornRadii,
+ (bNS ? GMX_FORCE_NS : 0) | force_flags);
+ }
+
+ if (bVV && !bStartingFromCpt && !bRerunMD)
+ /* ############### START FIRST UPDATE HALF-STEP FOR VV METHODS############### */
+ {
+ if (ir->eI == eiVV && bInitStep)
+ {
+ /* if using velocity verlet with full time step Ekin,
+ * take the first half step only to compute the
+ * virial for the first step. From there,
+ * revert back to the initial coordinates
+ * so that the input is actually the initial step.
+ */
+ copy_rvecn(state->v, cbuf, 0, state->natoms); /* should make this better for parallelizing? */
+ }
+ else
+ {
+ /* this is for NHC in the Ekin(t+dt/2) version of vv */
+ trotter_update(ir, step, ekind, enerd, state, total_vir, mdatoms, &MassQ, trotter_seq, ettTSEQ1);
+ }
+
+ /* If we are using twin-range interactions where the long-range component
+ * is only evaluated every nstcalclr>1 steps, we should do a special update
+ * step to combine the long-range forces on these steps.
+ * For nstcalclr=1 this is not done, since the forces would have been added
+ * directly to the short-range forces already.
++ *
++ * TODO Remove various aspects of VV+twin-range in master
++ * branch, because VV integrators did not ever support
++ * twin-range multiple time stepping with constraints.
+ */
+ bUpdateDoLR = (fr->bTwinRange && do_per_step(step, ir->nstcalclr));
+
+ update_coords(fplog, step, ir, mdatoms, state, fr->bMolPBC,
+ f, bUpdateDoLR, fr->f_twin, fcd,
+ ekind, M, upd, bInitStep, etrtVELOCITY1,
+ cr, nrnb, constr, &top->idef);
+
+ if (bIterativeCase && do_per_step(step-1, ir->nstpcouple) && !bInitStep)
+ {
+ gmx_iterate_init(&iterate, TRUE);
+ }
+ /* for iterations, we save these vectors, as we will be self-consistently iterating
+ the calculations */
+
+ /*#### UPDATE EXTENDED VARIABLES IN TROTTER FORMULATION */
+
+ /* save the state */
+ if (iterate.bIterationActive)
+ {
+ copy_coupling_state(state, bufstate, ekind, ekind_save, &(ir->opts));
+ }
+
+ bFirstIterate = TRUE;
+ while (bFirstIterate || iterate.bIterationActive)
+ {
+ if (iterate.bIterationActive)
+ {
+ copy_coupling_state(bufstate, state, ekind_save, ekind, &(ir->opts));
+ if (bFirstIterate && bTrotter)
+ {
+ /* The first time through, we need a decent first estimate
+ of veta(t+dt) to compute the constraints. Do
+ this by computing the box volume part of the
+ trotter integration at this time. Nothing else
+ should be changed by this routine here. If
+ !(first time), we start with the previous value
+ of veta. */
+
+ veta_save = state->veta;
+ trotter_update(ir, step, ekind, enerd, state, total_vir, mdatoms, &MassQ, trotter_seq, ettTSEQ0);
+ vetanew = state->veta;
+ state->veta = veta_save;
+ }
+ }
+
+ bOK = TRUE;
+ if (!bRerunMD || rerun_fr.bV || bForceUpdate) /* Why is rerun_fr.bV here? Unclear. */
+ {
+ update_constraints(fplog, step, NULL, ir, ekind, mdatoms,
+ state, fr->bMolPBC, graph, f,
+ &top->idef, shake_vir,
+ cr, nrnb, wcycle, upd, constr,
+ TRUE, bCalcVir, vetanew);
+
+ if (!bOK)
+ {
+ gmx_fatal(FARGS, "Constraint error: Shake, Lincs or Settle could not solve the constrains");
+ }
+
+ }
+ else if (graph)
+ {
+ /* Need to unshift here if a do_force has been
+ called in the previous step */
+ unshift_self(graph, state->box, state->x);
+ }
+
+ /* if VV, compute the pressure and constraints */
+ /* For VV2, we strictly only need this if using pressure
+ * control, but we really would like to have accurate pressures
+ * printed out.
+ * Think about ways around this in the future?
+ * For now, keep this choice in comments.
+ */
+ /*bPres = (ir->eI==eiVV || IR_NPT_TROTTER(ir)); */
+ /*bTemp = ((ir->eI==eiVV &&(!bInitStep)) || (ir->eI==eiVVAK && IR_NPT_TROTTER(ir)));*/
+ bPres = TRUE;
+ bTemp = ((ir->eI == eiVV && (!bInitStep)) || (ir->eI == eiVVAK));
+ if (bCalcEner && ir->eI == eiVVAK) /*MRS: 7/9/2010 -- this still doesn't fix it?*/
+ {
+ bSumEkinhOld = TRUE;
+ }
+ /* for vv, the first half of the integration actually corresponds to the previous step.
+ So we need information from the last step in the first half of the integration */
+ if (bGStat || do_per_step(step-1, nstglobalcomm))
+ {
+ compute_globals(fplog, gstat, cr, ir, fr, ekind, state, state_global, mdatoms, nrnb, vcm,
+ wcycle, enerd, force_vir, shake_vir, total_vir, pres, mu_tot,
+ constr, NULL, FALSE, state->box,
+ top_global, &bSumEkinhOld,
+ cglo_flags
+ | CGLO_ENERGY
+ | (bTemp ? CGLO_TEMPERATURE : 0)
+ | (bPres ? CGLO_PRESSURE : 0)
+ | (bPres ? CGLO_CONSTRAINT : 0)
+ | ((iterate.bIterationActive) ? CGLO_ITERATE : 0)
+ | (bFirstIterate ? CGLO_FIRSTITERATE : 0)
+ | CGLO_SCALEEKIN
+ );
+ /* explanation of above:
+ a) We compute Ekin at the full time step
+ if 1) we are using the AveVel Ekin, and it's not the
+ initial step, or 2) if we are using AveEkin, but need the full
+ time step kinetic energy for the pressure (always true now, since we want accurate statistics).
+ b) If we are using EkinAveEkin for the kinetic energy for the temperature control, we still feed in
+ EkinAveVel because it's needed for the pressure */
+ }
+ /* temperature scaling and pressure scaling to produce the extended variables at t+dt */
+ if (!bInitStep)
+ {
+ if (bTrotter)
+ {
+ m_add(force_vir, shake_vir, total_vir); /* we need the un-dispersion corrected total vir here */
+ trotter_update(ir, step, ekind, enerd, state, total_vir, mdatoms, &MassQ, trotter_seq, ettTSEQ2);
+ }
+ else
+ {
+ if (bExchanged)
+ {
+
+ /* We need the kinetic energy at minus the half step for determining
+ * the full step kinetic energy and possibly for T-coupling.*/
+ /* This may not be quite working correctly yet . . . . */
+ compute_globals(fplog, gstat, cr, ir, fr, ekind, state, state_global, mdatoms, nrnb, vcm,
+ wcycle, enerd, NULL, NULL, NULL, NULL, mu_tot,
+ constr, NULL, FALSE, state->box,
+ top_global, &bSumEkinhOld,
+ CGLO_RERUNMD | CGLO_GSTAT | CGLO_TEMPERATURE);
+ }
+ }
+ }
+
+ if (iterate.bIterationActive &&
+ done_iterating(cr, fplog, step, &iterate, bFirstIterate,
+ state->veta, &vetanew))
+ {
+ break;
+ }
+ bFirstIterate = FALSE;
+ }
+
+ if (bTrotter && !bInitStep)
+ {
+ copy_mat(shake_vir, state->svir_prev);
+ copy_mat(force_vir, state->fvir_prev);
+ if (IR_NVT_TROTTER(ir) && ir->eI == eiVV)
+ {
+ /* update temperature and kinetic energy now that step is over - this is the v(t+dt) point */
+ enerd->term[F_TEMP] = sum_ekin(&(ir->opts), ekind, NULL, (ir->eI == eiVV), FALSE);
+ enerd->term[F_EKIN] = trace(ekind->ekin);
+ }
+ }
+ /* if it's the initial step, we performed this first step just to get the constraint virial */
+ if (bInitStep && ir->eI == eiVV)
+ {
+ copy_rvecn(cbuf, state->v, 0, state->natoms);
+ }
+ }
+
+ /* MRS -- now done iterating -- compute the conserved quantity */
+ if (bVV)
+ {
+ saved_conserved_quantity = compute_conserved_from_auxiliary(ir, state, &MassQ);
+ if (ir->eI == eiVV)
+ {
+ last_ekin = enerd->term[F_EKIN];
+ }
+ if ((ir->eDispCorr != edispcEnerPres) && (ir->eDispCorr != edispcAllEnerPres))
+ {
+ saved_conserved_quantity -= enerd->term[F_DISPCORR];
+ }
+ /* sum up the foreign energy and dhdl terms for vv. currently done every step so that dhdl is correct in the .edr */
+ if (!bRerunMD)
+ {
+ sum_dhdl(enerd, state->lambda, ir->fepvals);
+ }
+ }
+
+ /* ######## END FIRST UPDATE STEP ############## */
+ /* ######## If doing VV, we now have v(dt) ###### */
+ if (bDoExpanded)
+ {
+ /* perform extended ensemble sampling in lambda - we don't
+ actually move to the new state before outputting
+ statistics, but if performing simulated tempering, we
+ do update the velocities and the tau_t. */
+
+ lamnew = ExpandedEnsembleDynamics(fplog, ir, enerd, state, &MassQ, state->fep_state, &state->dfhist, step, state->v, mdatoms);
+ /* history is maintained in state->dfhist, but state_global is what is sent to trajectory and log output */
+ copy_df_history(&state_global->dfhist, &state->dfhist);
+ }
+
+ /* Now we have the energies and forces corresponding to the
+ * coordinates at time t. We must output all of this before
+ * the update.
+ */
+ do_md_trajectory_writing(fplog, cr, nfile, fnm, step, step_rel, t,
+ ir, state, state_global, top_global, fr,
+ outf, mdebin, ekind, f, f_global,
+ wcycle, &nchkpt,
+ bCPT, bRerunMD, bLastStep, (Flags & MD_CONFOUT),
+ bSumEkinhOld);
+ /* Check if IMD step and do IMD communication, if bIMD is TRUE. */
+ bIMDstep = do_IMD(ir->bIMD, step, cr, bNS, state->box, state->x, ir, t, wcycle);
+
+ /* kludge -- virial is lost with restart for NPT control. Must restart */
+ if (bStartingFromCpt && bVV)
+ {
+ copy_mat(state->svir_prev, shake_vir);
+ copy_mat(state->fvir_prev, force_vir);
+ }
+
+ elapsed_time = walltime_accounting_get_current_elapsed_time(walltime_accounting);
+
+ /* Check whether everything is still allright */
+ if (((int)gmx_get_stop_condition() > handled_stop_condition)
+#ifdef GMX_THREAD_MPI
+ && MASTER(cr)
+#endif
+ )
+ {
+ /* this is just make gs.sig compatible with the hack
+ of sending signals around by MPI_Reduce with together with
+ other floats */
+ if (gmx_get_stop_condition() == gmx_stop_cond_next_ns)
+ {
+ gs.sig[eglsSTOPCOND] = 1;
+ }
+ if (gmx_get_stop_condition() == gmx_stop_cond_next)
+ {
+ gs.sig[eglsSTOPCOND] = -1;
+ }
+ /* < 0 means stop at next step, > 0 means stop at next NS step */
+ if (fplog)
+ {
+ fprintf(fplog,
+ "\n\nReceived the %s signal, stopping at the next %sstep\n\n",
+ gmx_get_signal_name(),
+ gs.sig[eglsSTOPCOND] == 1 ? "NS " : "");
+ fflush(fplog);
+ }
+ fprintf(stderr,
+ "\n\nReceived the %s signal, stopping at the next %sstep\n\n",
+ gmx_get_signal_name(),
+ gs.sig[eglsSTOPCOND] == 1 ? "NS " : "");
+ fflush(stderr);
+ handled_stop_condition = (int)gmx_get_stop_condition();
+ }
+ else if (MASTER(cr) && (bNS || ir->nstlist <= 0) &&
+ (max_hours > 0 && elapsed_time > max_hours*60.0*60.0*0.99) &&
+ gs.sig[eglsSTOPCOND] == 0 && gs.set[eglsSTOPCOND] == 0)
+ {
+ /* Signal to terminate the run */
+ gs.sig[eglsSTOPCOND] = 1;
+ if (fplog)
+ {
+ fprintf(fplog, "\nStep %s: Run time exceeded %.3f hours, will terminate the run\n", gmx_step_str(step, sbuf), max_hours*0.99);
+ }
+ fprintf(stderr, "\nStep %s: Run time exceeded %.3f hours, will terminate the run\n", gmx_step_str(step, sbuf), max_hours*0.99);
+ }
+
+ if (bResetCountersHalfMaxH && MASTER(cr) &&
+ elapsed_time > max_hours*60.0*60.0*0.495)
+ {
+ gs.sig[eglsRESETCOUNTERS] = 1;
+ }
+
+ if (ir->nstlist == -1 && !bRerunMD)
+ {
+ /* When bGStatEveryStep=FALSE, global_stat is only called
+ * when we check the atom displacements, not at NS steps.
+ * This means that also the bonded interaction count check is not
+ * performed immediately after NS. Therefore a few MD steps could
+ * be performed with missing interactions.
+ * But wrong energies are never written to file,
+ * since energies are only written after global_stat
+ * has been called.
+ */
+ if (step >= nlh.step_nscheck)
+ {
+ nlh.nabnsb = natoms_beyond_ns_buffer(ir, fr, &top->cgs,
+ nlh.scale_tot, state->x);
+ }
+ else
+ {
+ /* This is not necessarily true,
+ * but step_nscheck is determined quite conservatively.
+ */
+ nlh.nabnsb = 0;
+ }
+ }
+
+ /* In parallel we only have to check for checkpointing in steps
+ * where we do global communication,
+ * otherwise the other nodes don't know.
+ */
+ if (MASTER(cr) && ((bGStat || !PAR(cr)) &&
+ cpt_period >= 0 &&
+ (cpt_period == 0 ||
+ elapsed_time >= nchkpt*cpt_period*60.0)) &&
+ gs.set[eglsCHKPT] == 0)
+ {
+ gs.sig[eglsCHKPT] = 1;
+ }
+
+ /* at the start of step, randomize or scale the velocities (trotter done elsewhere) */
+ if (EI_VV(ir->eI))
+ {
+ if (!bInitStep)
+ {
+ update_tcouple(step, ir, state, ekind, &MassQ, mdatoms);
+ }
+ if (ETC_ANDERSEN(ir->etc)) /* keep this outside of update_tcouple because of the extra info required to pass */
+ {
+ gmx_bool bIfRandomize;
+ bIfRandomize = update_randomize_velocities(ir, step, cr, mdatoms, state, upd, constr);
+ /* if we have constraints, we have to remove the kinetic energy parallel to the bonds */
+ if (constr && bIfRandomize)
+ {
+ update_constraints(fplog, step, NULL, ir, ekind, mdatoms,
+ state, fr->bMolPBC, graph, f,
+ &top->idef, tmp_vir,
+ cr, nrnb, wcycle, upd, constr,
+ TRUE, bCalcVir, vetanew);
+ }
+ }
+ }
+
+ if (bIterativeCase && do_per_step(step, ir->nstpcouple))
+ {
+ gmx_iterate_init(&iterate, TRUE);
+ /* for iterations, we save these vectors, as we will be redoing the calculations */
+ copy_coupling_state(state, bufstate, ekind, ekind_save, &(ir->opts));
+ }
+
+ bFirstIterate = TRUE;
+ while (bFirstIterate || iterate.bIterationActive)
+ {
+ /* We now restore these vectors to redo the calculation with improved extended variables */
+ if (iterate.bIterationActive)
+ {
+ copy_coupling_state(bufstate, state, ekind_save, ekind, &(ir->opts));
+ }
+
+ /* We make the decision to break or not -after- the calculation of Ekin and Pressure,
+ so scroll down for that logic */
+
+ /* ######### START SECOND UPDATE STEP ################# */
+ /* Box is changed in update() when we do pressure coupling,
+ * but we should still use the old box for energy corrections and when
+ * writing it to the energy file, so it matches the trajectory files for
+ * the same timestep above. Make a copy in a separate array.
+ */
+ copy_mat(state->box, lastbox);
+
+ bOK = TRUE;
+ dvdl_constr = 0;
+
+ if (!(bRerunMD && !rerun_fr.bV && !bForceUpdate))
+ {
+ wallcycle_start(wcycle, ewcUPDATE);
+ /* UPDATE PRESSURE VARIABLES IN TROTTER FORMULATION WITH CONSTRAINTS */
+ if (bTrotter)
+ {
+ if (iterate.bIterationActive)
+ {
+ if (bFirstIterate)
+ {
+ scalevir = 1;
+ }
+ else
+ {
+ /* we use a new value of scalevir to converge the iterations faster */
+ scalevir = tracevir/trace(shake_vir);
+ }
+ msmul(shake_vir, scalevir, shake_vir);
+ m_add(force_vir, shake_vir, total_vir);
+ clear_mat(shake_vir);
+ }
+ trotter_update(ir, step, ekind, enerd, state, total_vir, mdatoms, &MassQ, trotter_seq, ettTSEQ3);
+ /* We can only do Berendsen coupling after we have summed
+ * the kinetic energy or virial. Since the happens
+ * in global_state after update, we should only do it at
+ * step % nstlist = 1 with bGStatEveryStep=FALSE.
+ */
+ }
+ else
+ {
+ update_tcouple(step, ir, state, ekind, &MassQ, mdatoms);
+ update_pcouple(fplog, step, ir, state, pcoupl_mu, M, bInitStep);
+ }
+
+ if (bVV)
+ {
+ bUpdateDoLR = (fr->bTwinRange && do_per_step(step, ir->nstcalclr));
+
+ /* velocity half-step update */
+ update_coords(fplog, step, ir, mdatoms, state, fr->bMolPBC, f,
+ bUpdateDoLR, fr->f_twin, fcd,
+ ekind, M, upd, FALSE, etrtVELOCITY2,
+ cr, nrnb, constr, &top->idef);
+ }
+
+ /* Above, initialize just copies ekinh into ekin,
+ * it doesn't copy position (for VV),
+ * and entire integrator for MD.
+ */
+
+ if (ir->eI == eiVVAK)
+ {
+ copy_rvecn(state->x, cbuf, 0, state->natoms);
+ }
+ bUpdateDoLR = (fr->bTwinRange && do_per_step(step, ir->nstcalclr));
+
+ update_coords(fplog, step, ir, mdatoms, state, fr->bMolPBC, f,
+ bUpdateDoLR, fr->f_twin, fcd,
+ ekind, M, upd, bInitStep, etrtPOSITION, cr, nrnb, constr, &top->idef);
+ wallcycle_stop(wcycle, ewcUPDATE);
+
+ update_constraints(fplog, step, &dvdl_constr, ir, ekind, mdatoms, state,
+ fr->bMolPBC, graph, f,
+ &top->idef, shake_vir,
+ cr, nrnb, wcycle, upd, constr,
+ FALSE, bCalcVir, state->veta);
+
+ if (ir->eI == eiVVAK)
+ {
+ /* erase F_EKIN and F_TEMP here? */
+ /* just compute the kinetic energy at the half step to perform a trotter step */
+ compute_globals(fplog, gstat, cr, ir, fr, ekind, state, state_global, mdatoms, nrnb, vcm,
+ wcycle, enerd, force_vir, shake_vir, total_vir, pres, mu_tot,
+ constr, NULL, FALSE, lastbox,
+ top_global, &bSumEkinhOld,
+ cglo_flags | CGLO_TEMPERATURE
+ );
+ wallcycle_start(wcycle, ewcUPDATE);
+ trotter_update(ir, step, ekind, enerd, state, total_vir, mdatoms, &MassQ, trotter_seq, ettTSEQ4);
+ /* now we know the scaling, we can compute the positions again again */
+ copy_rvecn(cbuf, state->x, 0, state->natoms);
+
+ bUpdateDoLR = (fr->bTwinRange && do_per_step(step, ir->nstcalclr));
+
+ update_coords(fplog, step, ir, mdatoms, state, fr->bMolPBC, f,
+ bUpdateDoLR, fr->f_twin, fcd,
+ ekind, M, upd, bInitStep, etrtPOSITION, cr, nrnb, constr, &top->idef);
+ wallcycle_stop(wcycle, ewcUPDATE);
+
+ /* do we need an extra constraint here? just need to copy out of state->v to upd->xp? */
+ /* are the small terms in the shake_vir here due
+ * to numerical errors, or are they important
+ * physically? I'm thinking they are just errors, but not completely sure.
+ * For now, will call without actually constraining, constr=NULL*/
+ update_constraints(fplog, step, NULL, ir, ekind, mdatoms,
+ state, fr->bMolPBC, graph, f,
+ &top->idef, tmp_vir,
+ cr, nrnb, wcycle, upd, NULL,
+ FALSE, bCalcVir,
+ state->veta);
+ }
+ if (!bOK)
+ {
+ gmx_fatal(FARGS, "Constraint error: Shake, Lincs or Settle could not solve the constrains");
+ }
+
+ if (fr->bSepDVDL && fplog && do_log)
+ {
+ gmx_print_sepdvdl(fplog, "Constraint dV/dl", 0.0, dvdl_constr);
+ }
+ if (bVV)
+ {
+ /* this factor or 2 correction is necessary
+ because half of the constraint force is removed
+ in the vv step, so we have to double it. See
+ the Redmine issue #1255. It is not yet clear
+ if the factor of 2 is exact, or just a very
+ good approximation, and this will be
+ investigated. The next step is to see if this
+ can be done adding a dhdl contribution from the
+ rattle step, but this is somewhat more
+ complicated with the current code. Will be
+ investigated, hopefully for 4.6.3. However,
+ this current solution is much better than
+ having it completely wrong.
+ */
+ enerd->term[F_DVDL_CONSTR] += 2*dvdl_constr;
+ }
+ else
+ {
+ enerd->term[F_DVDL_CONSTR] += dvdl_constr;
+ }
+ }
+ else if (graph)
+ {
+ /* Need to unshift here */
+ unshift_self(graph, state->box, state->x);
+ }
+
+ if (vsite != NULL)
+ {
+ wallcycle_start(wcycle, ewcVSITECONSTR);
+ if (graph != NULL)
+ {
+ shift_self(graph, state->box, state->x);
+ }
+ construct_vsites(vsite, state->x, ir->delta_t, state->v,
+ top->idef.iparams, top->idef.il,
+ fr->ePBC, fr->bMolPBC, cr, state->box);
+
+ if (graph != NULL)
+ {
+ unshift_self(graph, state->box, state->x);
+ }
+ wallcycle_stop(wcycle, ewcVSITECONSTR);
+ }
+
+ /* ############## IF NOT VV, Calculate globals HERE, also iterate constraints ############ */
+ /* With Leap-Frog we can skip compute_globals at
+ * non-communication steps, but we need to calculate
+ * the kinetic energy one step before communication.
+ */
+ if (bGStat || (!EI_VV(ir->eI) && do_per_step(step+1, nstglobalcomm)))
+ {
+ if (ir->nstlist == -1 && bFirstIterate)
+ {
+ gs.sig[eglsNABNSB] = nlh.nabnsb;
+ }
+ compute_globals(fplog, gstat, cr, ir, fr, ekind, state, state_global, mdatoms, nrnb, vcm,
+ wcycle, enerd, force_vir, shake_vir, total_vir, pres, mu_tot,
+ constr,
+ bFirstIterate ? &gs : NULL,
+ (step_rel % gs.nstms == 0) &&
+ (multisim_nsteps < 0 || (step_rel < multisim_nsteps)),
+ lastbox,
+ top_global, &bSumEkinhOld,
+ cglo_flags
+ | (!EI_VV(ir->eI) || bRerunMD ? CGLO_ENERGY : 0)
+ | (!EI_VV(ir->eI) && bStopCM ? CGLO_STOPCM : 0)
+ | (!EI_VV(ir->eI) ? CGLO_TEMPERATURE : 0)
+ | (!EI_VV(ir->eI) || bRerunMD ? CGLO_PRESSURE : 0)
+ | (iterate.bIterationActive ? CGLO_ITERATE : 0)
+ | (bFirstIterate ? CGLO_FIRSTITERATE : 0)
+ | CGLO_CONSTRAINT
+ );
+ if (ir->nstlist == -1 && bFirstIterate)
+ {
+ nlh.nabnsb = gs.set[eglsNABNSB];
+ gs.set[eglsNABNSB] = 0;
+ }
+ }
+ /* bIterate is set to keep it from eliminating the old ekin kinetic energy terms */
+ /* ############# END CALC EKIN AND PRESSURE ################# */
+
+ /* Note: this is OK, but there are some numerical precision issues with using the convergence of
+ the virial that should probably be addressed eventually. state->veta has better properies,
+ but what we actually need entering the new cycle is the new shake_vir value. Ideally, we could
+ generate the new shake_vir, but test the veta value for convergence. This will take some thought. */
+
+ if (iterate.bIterationActive &&
+ done_iterating(cr, fplog, step, &iterate, bFirstIterate,
+ trace(shake_vir), &tracevir))
+ {
+ break;
+ }
+ bFirstIterate = FALSE;
+ }
+
+ if (!bVV || bRerunMD)
+ {
+ /* sum up the foreign energy and dhdl terms for md and sd. currently done every step so that dhdl is correct in the .edr */
+ sum_dhdl(enerd, state->lambda, ir->fepvals);
+ }
+ update_box(fplog, step, ir, mdatoms, state, f,
+ ir->nstlist == -1 ? &nlh.scale_tot : NULL, pcoupl_mu, nrnb, upd);
+
+ /* ################# END UPDATE STEP 2 ################# */
+ /* #### We now have r(t+dt) and v(t+dt/2) ############# */
+
+ /* The coordinates (x) were unshifted in update */
+ if (!bGStat)
+ {
+ /* We will not sum ekinh_old,
+ * so signal that we still have to do it.
+ */
+ bSumEkinhOld = TRUE;
+ }
+
+ /* ######### BEGIN PREPARING EDR OUTPUT ########### */
+
+ /* use the directly determined last velocity, not actually the averaged half steps */
+ if (bTrotter && ir->eI == eiVV)
+ {
+ enerd->term[F_EKIN] = last_ekin;
+ }
+ enerd->term[F_ETOT] = enerd->term[F_EPOT] + enerd->term[F_EKIN];
+
+ if (bVV)
+ {
+ enerd->term[F_ECONSERVED] = enerd->term[F_ETOT] + saved_conserved_quantity;
+ }
+ else
+ {
+ enerd->term[F_ECONSERVED] = enerd->term[F_ETOT] + compute_conserved_from_auxiliary(ir, state, &MassQ);
+ }
+ /* ######### END PREPARING EDR OUTPUT ########### */
+
+ /* Output stuff */
+ if (MASTER(cr))
+ {
+ gmx_bool do_dr, do_or;
+
+ if (fplog && do_log && bDoExpanded)
+ {
+ /* only needed if doing expanded ensemble */
+ PrintFreeEnergyInfoToFile(fplog, ir->fepvals, ir->expandedvals, ir->bSimTemp ? ir->simtempvals : NULL,
+ &state_global->dfhist, state->fep_state, ir->nstlog, step);
+ }
+ if (!(bStartingFromCpt && (EI_VV(ir->eI))))
+ {
+ if (bCalcEner)
+ {
+ upd_mdebin(mdebin, bDoDHDL, TRUE,
+ t, mdatoms->tmass, enerd, state,
+ ir->fepvals, ir->expandedvals, lastbox,
+ shake_vir, force_vir, total_vir, pres,
+ ekind, mu_tot, constr);
+ }
+ else
+ {
+ upd_mdebin_step(mdebin);
+ }
+
+ do_dr = do_per_step(step, ir->nstdisreout);
+ do_or = do_per_step(step, ir->nstorireout);
+
+ print_ebin(mdoutf_get_fp_ene(outf), do_ene, do_dr, do_or, do_log ? fplog : NULL,
+ step, t,
+ eprNORMAL, bCompact, mdebin, fcd, groups, &(ir->opts));
+ }
+ if (ir->ePull != epullNO)
+ {
+ pull_print_output(ir->pull, step, t);
+ }
+
+ if (do_per_step(step, ir->nstlog))
+ {
+ if (fflush(fplog) != 0)
+ {
+ gmx_fatal(FARGS, "Cannot flush logfile - maybe you are out of disk space?");
+ }
+ }
+ }
+ if (bDoExpanded)
+ {
+ /* Have to do this part _after_ outputting the logfile and the edr file */
+ /* Gets written into the state at the beginning of next loop*/
+ state->fep_state = lamnew;
+ }
+ /* Print the remaining wall clock time for the run */
+ if (MULTIMASTER(cr) && (do_verbose || gmx_got_usr_signal()) && !bPMETuneRunning)
+ {
+ if (shellfc)
+ {
+ fprintf(stderr, "\n");
+ }
+ print_time(stderr, walltime_accounting, step, ir, cr);
+ }
+
+ /* Ion/water position swapping.
+ * Not done in last step since trajectory writing happens before this call
+ * in the MD loop and exchanges would be lost anyway. */
+ bNeedRepartition = FALSE;
+ if ((ir->eSwapCoords != eswapNO) && (step > 0) && !bLastStep &&
+ do_per_step(step, ir->swap->nstswap))
+ {
+ bNeedRepartition = do_swapcoords(cr, step, t, ir, wcycle,
+ bRerunMD ? rerun_fr.x : state->x,
+ bRerunMD ? rerun_fr.box : state->box,
+ top_global, MASTER(cr) && bVerbose, bRerunMD);
+
+ if (bNeedRepartition && DOMAINDECOMP(cr))
+ {
+ dd_collect_state(cr->dd, state, state_global);
+ }
+ }
+
+ /* Replica exchange */
+ bExchanged = FALSE;
+ if ((repl_ex_nst > 0) && (step > 0) && !bLastStep &&
+ do_per_step(step, repl_ex_nst))
+ {
+ bExchanged = replica_exchange(fplog, cr, repl_ex,
+ state_global, enerd,
+ state, step, t);
+ }
+
+ if ( (bExchanged || bNeedRepartition) && DOMAINDECOMP(cr) )
+ {
+ dd_partition_system(fplog, step, cr, TRUE, 1,
+ state_global, top_global, ir,
+ state, &f, mdatoms, top, fr,
+ vsite, shellfc, constr,
+ nrnb, wcycle, FALSE);
+ }
+
+ bFirstStep = FALSE;
+ bInitStep = FALSE;
+ bStartingFromCpt = FALSE;
+
+ /* ####### SET VARIABLES FOR NEXT ITERATION IF THEY STILL NEED IT ###### */
+ /* With all integrators, except VV, we need to retain the pressure
+ * at the current step for coupling at the next step.
+ */
+ if ((state->flags & (1<<estPRES_PREV)) &&
+ (bGStatEveryStep ||
+ (ir->nstpcouple > 0 && step % ir->nstpcouple == 0)))
+ {
+ /* Store the pressure in t_state for pressure coupling
+ * at the next MD step.
+ */
+ copy_mat(pres, state->pres_prev);
+ }
+
+ /* ####### END SET VARIABLES FOR NEXT ITERATION ###### */
+
+ if ( (membed != NULL) && (!bLastStep) )
+ {
+ rescale_membed(step_rel, membed, state_global->x);
+ }
+
+ if (bRerunMD)
+ {
+ if (MASTER(cr))
+ {
+ /* read next frame from input trajectory */
+ bNotLastFrame = read_next_frame(oenv, status, &rerun_fr);
+ }
+
+ if (PAR(cr))
+ {
+ rerun_parallel_comm(cr, &rerun_fr, &bNotLastFrame);
+ }
+ }
+
+ if (!bRerunMD || !rerun_fr.bStep)
+ {
+ /* increase the MD step number */
+ step++;
+ step_rel++;
+ }
+
+ cycles = wallcycle_stop(wcycle, ewcSTEP);
+ if (DOMAINDECOMP(cr) && wcycle)
+ {
+ dd_cycles_add(cr->dd, cycles, ddCyclStep);
+ }
+
+ if (bPMETuneRunning || bPMETuneTry)
+ {
+ /* PME grid + cut-off optimization with GPUs or PME nodes */
+
+ /* Count the total cycles over the last steps */
+ cycles_pmes += cycles;
+
+ /* We can only switch cut-off at NS steps */
+ if (step % ir->nstlist == 0)
+ {
+ /* PME grid + cut-off optimization with GPUs or PME nodes */
+ if (bPMETuneTry)
+ {
+ if (DDMASTER(cr->dd))
+ {
+ /* PME node load is too high, start tuning */
+ bPMETuneRunning = (dd_pme_f_ratio(cr->dd) >= 1.05);
+ }
+ dd_bcast(cr->dd, sizeof(gmx_bool), &bPMETuneRunning);
+
+ if (bPMETuneRunning || step_rel > ir->nstlist*50)
+ {
+ bPMETuneTry = FALSE;
+ }
+ }
+ if (bPMETuneRunning)
+ {
+ /* init_step might not be a multiple of nstlist,
+ * but the first cycle is always skipped anyhow.
+ */
+ bPMETuneRunning =
+ pme_load_balance(pme_loadbal, cr,
+ (bVerbose && MASTER(cr)) ? stderr : NULL,
+ fplog,
+ ir, state, cycles_pmes,
+ fr->ic, fr->nbv, &fr->pmedata,
+ step);
+
+ /* Update constants in forcerec/inputrec to keep them in sync with fr->ic */
+ fr->ewaldcoeff_q = fr->ic->ewaldcoeff_q;
+ fr->ewaldcoeff_lj = fr->ic->ewaldcoeff_lj;
+ fr->rlist = fr->ic->rlist;
+ fr->rlistlong = fr->ic->rlistlong;
+ fr->rcoulomb = fr->ic->rcoulomb;
+ fr->rvdw = fr->ic->rvdw;
+
+ if (ir->eDispCorr != edispcNO)
+ {
+ calc_enervirdiff(NULL, ir->eDispCorr, fr);
+ }
+ }
+ cycles_pmes = 0;
+ }
+ }
+
+ if (step_rel == wcycle_get_reset_counters(wcycle) ||
+ gs.set[eglsRESETCOUNTERS] != 0)
+ {
+ /* Reset all the counters related to performance over the run */
+ reset_all_counters(fplog, cr, step, &step_rel, ir, wcycle, nrnb, walltime_accounting,
+ fr->nbv != NULL && fr->nbv->bUseGPU ? fr->nbv->cu_nbv : NULL);
+ wcycle_set_reset_counters(wcycle, -1);
+ if (!(cr->duty & DUTY_PME))
+ {
+ /* Tell our PME node to reset its counters */
+ gmx_pme_send_resetcounters(cr, step);
+ }
+ /* Correct max_hours for the elapsed time */
+ max_hours -= elapsed_time/(60.0*60.0);
+ bResetCountersHalfMaxH = FALSE;
+ gs.set[eglsRESETCOUNTERS] = 0;
+ }
+
+ /* If bIMD is TRUE, the master updates the IMD energy record and sends positions to VMD client */
+ IMD_prep_energies_send_positions(ir->bIMD && MASTER(cr), bIMDstep, ir->imd, enerd, step, bCalcEner, wcycle);
+
+ }
+ /* End of main MD loop */
+ debug_gmx();
+
+ /* Stop measuring walltime */
+ walltime_accounting_end(walltime_accounting);
+
+ if (bRerunMD && MASTER(cr))
+ {
+ close_trj(status);
+ }
+
+ if (!(cr->duty & DUTY_PME))
+ {
+ /* Tell the PME only node to finish */
+ gmx_pme_send_finish(cr);
+ }
+
+ if (MASTER(cr))
+ {
+ if (ir->nstcalcenergy > 0 && !bRerunMD)
+ {
+ print_ebin(mdoutf_get_fp_ene(outf), FALSE, FALSE, FALSE, fplog, step, t,
+ eprAVER, FALSE, mdebin, fcd, groups, &(ir->opts));
+ }
+ }
+
+ done_mdoutf(outf);
+ debug_gmx();
+
+ if (ir->nstlist == -1 && nlh.nns > 0 && fplog)
+ {
+ fprintf(fplog, "Average neighborlist lifetime: %.1f steps, std.dev.: %.1f steps\n", nlh.s1/nlh.nns, sqrt(nlh.s2/nlh.nns - sqr(nlh.s1/nlh.nns)));
+ fprintf(fplog, "Average number of atoms that crossed the half buffer length: %.1f\n\n", nlh.ab/nlh.nns);
+ }
+
+ if (pme_loadbal != NULL)
+ {
+ pme_loadbal_done(pme_loadbal, cr, fplog,
+ fr->nbv != NULL && fr->nbv->bUseGPU);
+ }
+
+ if (shellfc && fplog)
+ {
+ fprintf(fplog, "Fraction of iterations that converged: %.2f %%\n",
+ (nconverged*100.0)/step_rel);
+ fprintf(fplog, "Average number of force evaluations per MD step: %.2f\n\n",
+ tcount/step_rel);
+ }
+
+ if (repl_ex_nst > 0 && MASTER(cr))
+ {
+ print_replica_exchange_statistics(fplog, repl_ex);
+ }
+
+ /* IMD cleanup, if bIMD is TRUE. */
+ IMD_finalize(ir->bIMD, ir->imd);
+
+ walltime_accounting_set_nsteps_done(walltime_accounting, step_rel);
+
+ return 0;
+}
biod.pnpi.spb.ru / alexxy / gromacs.git / commitdiff