# each release. It's hard to test because it is only used for
# REGRESSIONTEST_DOWNLOAD, which doesn't work until that tarball has
# been placed on the server.
- set(REGRESSIONTEST_MD5SUM "614a74e9b143bda5476f87f4ce08eec0" CACHE INTERNAL "MD5 sum of the regressiontests tarball")
+ set(REGRESSIONTEST_MD5SUM "3f663536649db883a5616f25f95ac927" CACHE INTERNAL "MD5 sum of the regressiontests tarball")
math(EXPR GMX_VERSION_NUMERIC
- "${GMX_VERSION_MAJOR}*10000 + ${GMX_VERSION_MINOR}*100 + ${GMX_VERSION_PATCH}")
+ "${GMX_VERSION_MAJOR}*10000 + ${GMX_VERSION_PATCH}")
set(GMX_API_VERSION ${GMX_VERSION_NUMERIC})
#####################################################################
/* Here we start a large thread parallel region */
#pragma omp parallel num_threads(pme->nthread) private(thread)
{
- thread = gmx_omp_get_thread_num();
- if (flags & GMX_PME_SOLVE)
+ try
{
- int loop_count;
-
- /* do 3d-fft */
- if (thread == 0)
- {
- wallcycle_start(wcycle, ewcPME_FFT);
- }
- gmx_parallel_3dfft_execute(pfft_setup, GMX_FFT_REAL_TO_COMPLEX,
- thread, wcycle);
- if (thread == 0)
- {
- wallcycle_stop(wcycle, ewcPME_FFT);
- }
- where();
-
- /* solve in k-space for our local cells */
- if (thread == 0)
- {
- wallcycle_start(wcycle, (grid_index < DO_Q ? ewcPME_SOLVE : ewcLJPME));
- }
- if (grid_index < DO_Q)
- {
- loop_count =
- solve_pme_yzx(pme, cfftgrid, ewaldcoeff_q,
- box[XX][XX]*box[YY][YY]*box[ZZ][ZZ],
- bCalcEnerVir,
- pme->nthread, thread);
- }
- else
+ thread = gmx_omp_get_thread_num();
+ if (flags & GMX_PME_SOLVE)
{
- loop_count =
- solve_pme_lj_yzx(pme, &cfftgrid, FALSE, ewaldcoeff_lj,
- box[XX][XX]*box[YY][YY]*box[ZZ][ZZ],
- bCalcEnerVir,
- pme->nthread, thread);
- }
+ int loop_count;
- if (thread == 0)
- {
- wallcycle_stop(wcycle, (grid_index < DO_Q ? ewcPME_SOLVE : ewcLJPME));
+ /* do 3d-fft */
+ if (thread == 0)
+ {
+ wallcycle_start(wcycle, ewcPME_FFT);
+ }
+ gmx_parallel_3dfft_execute(pfft_setup, GMX_FFT_REAL_TO_COMPLEX,
+ thread, wcycle);
+ if (thread == 0)
+ {
+ wallcycle_stop(wcycle, ewcPME_FFT);
+ }
where();
- inc_nrnb(nrnb, eNR_SOLVEPME, loop_count);
- }
- }
- if (bBackFFT)
- {
- /* do 3d-invfft */
- if (thread == 0)
- {
- where();
- wallcycle_start(wcycle, ewcPME_FFT);
+ /* solve in k-space for our local cells */
+ if (thread == 0)
+ {
+ wallcycle_start(wcycle, (grid_index < DO_Q ? ewcPME_SOLVE : ewcLJPME));
+ }
+ if (grid_index < DO_Q)
+ {
+ loop_count =
+ solve_pme_yzx(pme, cfftgrid, ewaldcoeff_q,
+ box[XX][XX]*box[YY][YY]*box[ZZ][ZZ],
+ bCalcEnerVir,
+ pme->nthread, thread);
+ }
+ else
+ {
+ loop_count =
+ solve_pme_lj_yzx(pme, &cfftgrid, FALSE, ewaldcoeff_lj,
+ box[XX][XX]*box[YY][YY]*box[ZZ][ZZ],
+ bCalcEnerVir,
+ pme->nthread, thread);
+ }
+
+ if (thread == 0)
+ {
+ wallcycle_stop(wcycle, (grid_index < DO_Q ? ewcPME_SOLVE : ewcLJPME));
+ where();
+ inc_nrnb(nrnb, eNR_SOLVEPME, loop_count);
+ }
}
- gmx_parallel_3dfft_execute(pfft_setup, GMX_FFT_COMPLEX_TO_REAL,
- thread, wcycle);
- if (thread == 0)
+
- if (bCalcF)
++ if (bBackFFT)
{
- wallcycle_stop(wcycle, ewcPME_FFT);
+ /* do 3d-invfft */
+ if (thread == 0)
+ {
+ where();
+ wallcycle_start(wcycle, ewcPME_FFT);
+ }
+ gmx_parallel_3dfft_execute(pfft_setup, GMX_FFT_COMPLEX_TO_REAL,
+ thread, wcycle);
+ if (thread == 0)
+ {
+ wallcycle_stop(wcycle, ewcPME_FFT);
- where();
+ where();
- if (pme->nodeid == 0)
- {
- real ntot = pme->nkx*pme->nky*pme->nkz;
- npme = static_cast<int>(ntot*log(ntot)/log(2.0));
- inc_nrnb(nrnb, eNR_FFT, 2*npme);
+ if (pme->nodeid == 0)
+ {
+ real ntot = pme->nkx*pme->nky*pme->nkz;
+ npme = static_cast<int>(ntot*log(ntot)/log(2.0));
+ inc_nrnb(nrnb, eNR_FFT, 2*npme);
+ }
+
+ /* Note: this wallcycle region is closed below
+ outside an OpenMP region, so take care if
+ refactoring code here. */
+ wallcycle_start(wcycle, ewcPME_SPREADGATHER);
}
- /* Note: this wallcycle region is closed below
- outside an OpenMP region, so take care if
- refactoring code here. */
- wallcycle_start(wcycle, ewcPME_SPREADGATHER);
+ copy_fftgrid_to_pmegrid(pme, fftgrid, grid, grid_index, pme->nthread, thread);
}
-
- copy_fftgrid_to_pmegrid(pme, fftgrid, grid, grid_index, pme->nthread, thread);
- }
+ } GMX_CATCH_ALL_AND_EXIT_WITH_FATAL_ERROR;
}
/* End of thread parallel section.
* With MPI we have to synchronize here before gmx_sum_qgrid_dd.
*/
- if (bCalcF)
+ if (bBackFFT)
{
/* distribute local grid to all nodes */
-#ifdef GMX_MPI
+#if GMX_MPI
if (pme->nnodes > 1)
{
gmx_sum_qgrid_dd(pme, grid, GMX_SUM_GRID_BACKWARD);
unwrap_periodic_pmegrid(pme, grid);
- /* interpolate forces for our local atoms */
- where();
- bClearF = (bFirst && PAR(cr));
- scale = pme->bFEP ? (fep_state < 1 ? 1.0-lambda_lj : lambda_lj) : 1.0;
- scale *= lb_scale_factor[grid_index-2];
- #pragma omp parallel for num_threads(pme->nthread) schedule(static)
- for (thread = 0; thread < pme->nthread; thread++)
+ if (bCalcF)
{
- try
+ /* interpolate forces for our local atoms */
+ where();
+ bClearF = (bFirst && PAR(cr));
+ scale = pme->bFEP ? (fep_state < 1 ? 1.0-lambda_lj : lambda_lj) : 1.0;
+ scale *= lb_scale_factor[grid_index-2];
++
+ #pragma omp parallel for num_threads(pme->nthread) schedule(static)
+ for (thread = 0; thread < pme->nthread; thread++)
{
-- gather_f_bsplines(pme, grid, bClearF, &pme->atc[0],
-- &pme->atc[0].spline[thread],
-- scale);
++ try
++ {
++ gather_f_bsplines(pme, grid, bClearF, &pme->atc[0],
++ &pme->atc[0].spline[thread],
++ scale);
++ }
++ GMX_CATCH_ALL_AND_EXIT_WITH_FATAL_ERROR;
}
- GMX_CATCH_ALL_AND_EXIT_WITH_FATAL_ERROR;
- }
- where();
+
- inc_nrnb(nrnb, eNR_GATHERFBSP,
- pme->pme_order*pme->pme_order*pme->pme_order*pme->atc[0].n);
+ where();
+
+ inc_nrnb(nrnb, eNR_GATHERFBSP,
+ pme->pme_order*pme->pme_order*pme->pme_order*pme->atc[0].n);
+ }
wallcycle_stop(wcycle, ewcPME_SPREADGATHER);
bFirst = FALSE;
--- /dev/null
- * Copyright (c) 2013,2014,2015, by the GROMACS development team, led by
+/*
+ * 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.
- if (ptr == (*inp)[ii].value)
++ * Copyright (c) 2013,2014,2015,2016, 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 "gmxpre.h"
+
+#include "readinp.h"
+
+#include <cstdio>
+#include <cstdlib>
+#include <cstring>
+
+#include <algorithm>
+
+#include "gromacs/fileio/gmxfio.h"
+#include "gromacs/fileio/warninp.h"
+#include "gromacs/mdtypes/md_enums.h"
+#include "gromacs/utility/binaryinformation.h"
+#include "gromacs/utility/cstringutil.h"
+#include "gromacs/utility/exceptions.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/futil.h"
+#include "gromacs/utility/programcontext.h"
+#include "gromacs/utility/qsort_threadsafe.h"
+#include "gromacs/utility/smalloc.h"
+
+t_inpfile *read_inpfile(const char *fn, int *ninp,
+ warninp_t wi)
+{
+ FILE *in;
+ char buf[STRLEN], lbuf[STRLEN], rbuf[STRLEN], warn_buf[STRLEN];
+ char *ptr, *cptr;
+ t_inpfile *inp = NULL;
+ int nin, lc, i, j, k;
+ /* setting cppopts from command-line options would be cooler */
+ gmx_bool allow_override = FALSE;
+
+
+ if (debug)
+ {
+ fprintf(debug, "Reading MDP file %s\n", fn);
+ }
+
+ in = gmx_ffopen(fn, "r");
+
+ nin = lc = 0;
+ do
+ {
+ ptr = fgets2(buf, STRLEN-1, in);
+ lc++;
+ set_warning_line(wi, fn, lc);
+ if (ptr)
+ {
++ // TODO This parsing should be using strip_comment, trim,
++ // strchr, etc. rather than re-inventing wheels.
++
+ /* Strip comment */
+ if ((cptr = std::strchr(buf, COMMENTSIGN)) != NULL)
+ {
+ *cptr = '\0';
+ }
+ /* Strip spaces */
+ trim(buf);
+
+ for (j = 0; (buf[j] != '=') && (buf[j] != '\0'); j++)
+ {
+ ;
+ }
+ if (buf[j] == '\0')
+ {
+ if (j > 0)
+ {
+ if (debug)
+ {
+ fprintf(debug, "No = on line %d in file %s, ignored\n", lc, fn);
+ }
+ }
+ }
+ else
+ {
+ for (i = 0; (i < j); i++)
+ {
+ lbuf[i] = buf[i];
+ }
+ lbuf[i] = '\0';
+ trim(lbuf);
+ if (lbuf[0] == '\0')
+ {
+ if (debug)
+ {
+ fprintf(debug, "Empty left hand side on line %d in file %s, ignored\n", lc, fn);
+ }
+ }
+ else
+ {
+ for (i = j+1, k = 0; (buf[i] != '\0'); i++, k++)
+ {
+ rbuf[k] = buf[i];
+ }
+ rbuf[k] = '\0';
+ trim(rbuf);
+ if (rbuf[0] == '\0')
+ {
+ if (debug)
+ {
+ fprintf(debug, "Empty right hand side on line %d in file %s, ignored\n", lc, fn);
+ }
+ }
+ else
+ {
+ /* Now finally something sensible */
+ int found_index;
+
+ /* first check whether we hit the 'multiple_entries' option */
+ if (gmx_strcasecmp_min(eMultentOpt_names[eMultentOptName], lbuf) == 0)
+ {
+ /* we now check whether to allow overrides from here or not */
+ if (gmx_strcasecmp_min(eMultentOpt_names[eMultentOptNo], rbuf) == 0)
+ {
+ allow_override = FALSE;
+ }
+ else if (gmx_strcasecmp_min(eMultentOpt_names[eMultentOptLast], rbuf) == 0)
+ {
+ allow_override = TRUE;
+ }
+ else
+ {
+ sprintf(warn_buf,
+ "Parameter \"%s\" should either be %s or %s\n",
+ lbuf,
+ eMultentOpt_names[eMultentOptNo],
+ eMultentOpt_names[eMultentOptLast]);
+ warning_error(wi, warn_buf);
+ }
+ }
+ else
+ {
+ /* it is a regular option; check for duplicates */
+ found_index = search_einp(nin, inp, lbuf);
+
+ if (found_index == -1)
+ {
+ /* add a new item */
+ srenew(inp, ++nin);
+ inp[nin-1].inp_count = 1;
+ inp[nin-1].count = 0;
+ inp[nin-1].bObsolete = FALSE;
+ inp[nin-1].bSet = FALSE;
+ inp[nin-1].name = gmx_strdup(lbuf);
+ inp[nin-1].value = gmx_strdup(rbuf);
+ }
+ else
+ {
+ if (!allow_override)
+ {
+ sprintf(warn_buf,
+ "Parameter \"%s\" doubly defined (and multiple assignments not allowed)\n",
+ lbuf);
+ warning_error(wi, warn_buf);
+ }
+ else
+ {
+ /* override */
+ if (!inp)
+ {
+ gmx_fatal(FARGS, "Internal inconsistency; inp[] base pointer is NULL");
+ }
+ sfree(inp[found_index].value);
+ inp[found_index].value = gmx_strdup(rbuf);
+ sprintf(warn_buf,
+ "Overriding existing parameter \"%s\" with value \"%s\"\n",
+ lbuf, rbuf);
+ warning_note(wi, warn_buf);
+ }
+ }
+ }
+ }
+ }
+ }
+ }
+ }
+ while (ptr);
+
+ gmx_ffclose(in);
+
+ if (debug)
+ {
+ fprintf(debug, "Done reading MDP file, there were %d entries in there\n",
+ nin);
+ }
+
+ *ninp = nin;
+
+ return inp;
+}
+
+
+
+
+static int inp_comp(const void *a, const void *b)
+{
+ return (reinterpret_cast<const t_inpfile *>(a))->count - (reinterpret_cast<const t_inpfile *>(b))->count;
+}
+
+static void sort_inp(int ninp, t_inpfile inp[])
+{
+ int i, mm;
+
+ mm = -1;
+ for (i = 0; (i < ninp); i++)
+ {
+ mm = std::max(mm, inp[i].count);
+ }
+ for (i = 0; (i < ninp); i++)
+ {
+ if (inp[i].count == 0)
+ {
+ inp[i].count = mm++;
+ }
+ }
+ gmx_qsort(inp, ninp, static_cast<size_t>(sizeof(inp[0])), inp_comp);
+}
+
+void write_inpfile(const char *fn, int ninp, t_inpfile inp[], gmx_bool bHaltOnUnknown,
+ warninp_t wi)
+{
+ FILE *out;
+ int i;
+ char warn_buf[STRLEN];
+
+ sort_inp(ninp, inp);
+ out = gmx_fio_fopen(fn, "w");
+ nice_header(out, fn);
+ try
+ {
+ gmx::BinaryInformationSettings settings;
+ settings.generatedByHeader(true);
+ settings.linePrefix(";\t");
+ gmx::printBinaryInformation(out, gmx::getProgramContext(), settings);
+ }
+ GMX_CATCH_ALL_AND_EXIT_WITH_FATAL_ERROR;
+
+ for (i = 0; (i < ninp); i++)
+ {
+ if (inp[i].bSet)
+ {
+ if (inp[i].name[0] == ';' || (strlen(inp[i].name) > 2 && inp[i].name[1] == ';'))
+ {
+ fprintf(out, "%-24s\n", inp[i].name);
+ }
+ else
+ {
+ fprintf(out, "%-24s = %s\n", inp[i].name, inp[i].value ? inp[i].value : "");
+ }
+ }
+ else if (!inp[i].bObsolete)
+ {
+ sprintf(warn_buf, "Unknown left-hand '%s' in parameter file\n",
+ inp[i].name);
+ if (bHaltOnUnknown)
+ {
+ warning_error(wi, warn_buf);
+ }
+ else
+ {
+ warning(wi, warn_buf);
+ }
+ }
+ }
+ gmx_fio_fclose(out);
+
+ check_warning_error(wi, FARGS);
+}
+
+void replace_inp_entry(int ninp, t_inpfile *inp, const char *old_entry, const char *new_entry)
+{
+ int i;
+
+ for (i = 0; (i < ninp); i++)
+ {
+ if (gmx_strcasecmp_min(old_entry, inp[i].name) == 0)
+ {
+ if (new_entry)
+ {
+ fprintf(stderr, "Replacing old mdp entry '%s' by '%s'\n",
+ inp[i].name, new_entry);
+ sfree(inp[i].name);
+ inp[i].name = gmx_strdup(new_entry);
+ }
+ else
+ {
+ fprintf(stderr, "Ignoring obsolete mdp entry '%s'\n",
+ inp[i].name);
+ inp[i].bObsolete = TRUE;
+ }
+ }
+ }
+}
+
+int search_einp(int ninp, const t_inpfile *inp, const char *name)
+{
+ int i;
+
+ if (inp == NULL)
+ {
+ return -1;
+ }
+ for (i = 0; i < ninp; i++)
+ {
+ if (gmx_strcasecmp_min(name, inp[i].name) == 0)
+ {
+ return i;
+ }
+ }
+ return -1;
+}
+
+static int get_einp(int *ninp, t_inpfile **inp, const char *name)
+{
+ int i;
+ int notfound = FALSE;
+
+ i = search_einp(*ninp, *inp, name);
+ if (i == -1)
+ {
+ notfound = TRUE;
+ i = (*ninp)++;
+ srenew(*inp, (*ninp));
+ (*inp)[i].name = gmx_strdup(name);
+ (*inp)[i].bSet = TRUE;
+ }
+ (*inp)[i].count = (*inp)[0].inp_count++;
+ (*inp)[i].bSet = TRUE;
+ if (debug)
+ {
+ fprintf(debug, "Inp %d = %s\n", (*inp)[i].count, (*inp)[i].name);
+ }
+
+ /*if (i == (*ninp)-1)*/
+ if (notfound)
+ {
+ return -1;
+ }
+ else
+ {
+ return i;
+ }
+}
+
++/* Note that sanitizing the trailing part of (*inp)[ii].value was the responsibility of read_inpfile() */
+int get_eint(int *ninp, t_inpfile **inp, const char *name, int def,
+ warninp_t wi)
+{
+ char buf[32], *ptr, warn_buf[STRLEN];
+ int ii;
+ int ret;
+
+ ii = get_einp(ninp, inp, name);
+
+ if (ii == -1)
+ {
+ sprintf(buf, "%d", def);
+ (*inp)[(*ninp)-1].value = gmx_strdup(buf);
+
+ return def;
+ }
+ else
+ {
+ ret = std::strtol((*inp)[ii].value, &ptr, 10);
- if (ptr == (*inp)[ii].value)
++ if (*ptr != '\0')
+ {
+ sprintf(warn_buf, "Right hand side '%s' for parameter '%s' in parameter file is not an integer value\n", (*inp)[ii].value, (*inp)[ii].name);
+ warning_error(wi, warn_buf);
+ }
+
+ return ret;
+ }
+}
+
++/* Note that sanitizing the trailing part of (*inp)[ii].value was the responsibility of read_inpfile() */
+gmx_int64_t get_eint64(int *ninp, t_inpfile **inp,
+ const char *name, gmx_int64_t def,
+ warninp_t wi)
+{
+ char buf[32], *ptr, warn_buf[STRLEN];
+ int ii;
+ gmx_int64_t ret;
+
+ ii = get_einp(ninp, inp, name);
+
+ if (ii == -1)
+ {
+ sprintf(buf, "%" GMX_PRId64, def);
+ (*inp)[(*ninp)-1].value = gmx_strdup(buf);
+
+ return def;
+ }
+ else
+ {
+ ret = str_to_int64_t((*inp)[ii].value, &ptr);
- if (ptr == (*inp)[ii].value)
++ if (*ptr != '\0')
+ {
+ sprintf(warn_buf, "Right hand side '%s' for parameter '%s' in parameter file is not an integer value\n", (*inp)[ii].value, (*inp)[ii].name);
+ warning_error(wi, warn_buf);
+ }
+
+ return ret;
+ }
+}
+
++/* Note that sanitizing the trailing part of (*inp)[ii].value was the responsibility of read_inpfile() */
+double get_ereal(int *ninp, t_inpfile **inp, const char *name, double def,
+ warninp_t wi)
+{
+ char buf[32], *ptr, warn_buf[STRLEN];
+ int ii;
+ double ret;
+
+ ii = get_einp(ninp, inp, name);
+
+ if (ii == -1)
+ {
+ sprintf(buf, "%g", def);
+ (*inp)[(*ninp)-1].value = gmx_strdup(buf);
+
+ return def;
+ }
+ else
+ {
+ ret = strtod((*inp)[ii].value, &ptr);
++ if (*ptr != '\0')
+ {
+ sprintf(warn_buf, "Right hand side '%s' for parameter '%s' in parameter file is not a real value\n", (*inp)[ii].value, (*inp)[ii].name);
+ warning_error(wi, warn_buf);
+ }
+
+ return ret;
+ }
+}
+
++/* Note that sanitizing the trailing part of (*inp)[ii].value was the responsibility of read_inpfile() */
+const char *get_estr(int *ninp, t_inpfile **inp, const char *name, const char *def)
+{
+ char buf[32];
+ int ii;
+
+ ii = get_einp(ninp, inp, name);
+
+ if (ii == -1)
+ {
+ if (def)
+ {
+ sprintf(buf, "%s", def);
+ (*inp)[(*ninp)-1].value = gmx_strdup(buf);
+ }
+ else
+ {
+ (*inp)[(*ninp)-1].value = NULL;
+ }
+
+ return def;
+ }
+ else
+ {
+ return (*inp)[ii].value;
+ }
+}
+
++/* Note that sanitizing the trailing part of (*inp)[ii].value was the responsibility of read_inpfile() */
+int get_eeenum(int *ninp, t_inpfile **inp, const char *name, const char **defs,
+ warninp_t wi)
+{
+ int ii, i, j;
+ int n = 0;
+ char buf[STRLEN];
+
+ ii = get_einp(ninp, inp, name);
+
+ if (ii == -1)
+ {
+ (*inp)[(*ninp)-1].value = gmx_strdup(defs[0]);
+
+ return 0;
+ }
+
+ for (i = 0; (defs[i] != NULL); i++)
+ {
+ if (gmx_strcasecmp_min(defs[i], (*inp)[ii].value) == 0)
+ {
+ break;
+ }
+ }
+
+ if (defs[i] == NULL)
+ {
+ n += sprintf(buf, "Invalid enum '%s' for variable %s, using '%s'\n",
+ (*inp)[ii].value, name, defs[0]);
+ n += sprintf(buf+n, "Next time use one of:");
+ j = 0;
+ while (defs[j])
+ {
+ n += sprintf(buf+n, " '%s'", defs[j]);
+ j++;
+ }
+ if (wi != NULL)
+ {
+ warning_error(wi, buf);
+ }
+ else
+ {
+ fprintf(stderr, "%s\n", buf);
+ }
+
+ (*inp)[ii].value = gmx_strdup(defs[0]);
+
+ return 0;
+ }
+
+ return i;
+}
+
+int get_eenum(int *ninp, t_inpfile **inp, const char *name, const char **defs)
+{
+ return get_eeenum(ninp, inp, name, defs, NULL);
+}
#
# This file is part of the GROMACS molecular simulation package.
#
- # Copyright (c) 2013,2014,2015, by the GROMACS development team, led by
-# Copyright (c) 2013,2014, by the GROMACS development team, led by
++# Copyright (c) 2013,2014,2015,2016, 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.
# To help us fund GROMACS development, we humbly ask that you cite
# the research papers on the package. Check out http://www.gromacs.org.
-if(GMX_USE_TNG)
- gmx_add_unit_test(FileIOTests fileio-test
- tngio.cpp)
+set(test_sources
+ confio.cpp
++ readinp.cpp
+ )
+if (GMX_USE_TNG)
+ list(APPEND test_sources tngio.cpp)
endif()
+gmx_add_unit_test(FileIOTests fileio-test ${test_sources})
--- /dev/null
--- /dev/null
++/*
++ * This file is part of the GROMACS molecular simulation package.
++ *
++ * Copyright (c) 2016, 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.
++ */
++/*! \internal \file
++ * \brief
++ * Tests utilities for routines that parse fields e.g. from grompp input
++ *
++ * \author Mark Abraham <mark.j.abraham@gmail.com>
++ */
++#include "gmxpre.h"
++
++#include "gromacs/fileio/readinp.h"
++
++#include <gtest/gtest.h>
++
++#include "gromacs/fileio/warninp.h"
++#include "gromacs/utility/scoped_cptr.h"
++#include "gromacs/utility/smalloc.h"
++
++namespace gmx
++{
++namespace testing
++{
++
++class ReadTest : public ::testing::Test
++{
++ public:
++ ReadTest() : numInputs_(1),
++ inputField_(0),
++ inpGuard_(),
++ wi_(),
++ wiGuard_()
++ {
++ snew(inputField_, numInputs_);
++ inpGuard_.reset(inputField_);
++
++ inputField_[0].count = 0;
++ inputField_[0].bObsolete = FALSE;
++ inputField_[0].bSet = FALSE;
++ inputField_[0].name = (char *) "test";
++ inputField_[0].inp_count = 0;
++
++ wi_ = init_warning(FALSE, 0);
++ wiGuard_.reset(wi_);
++ }
++
++ int numInputs_;
++ t_inpfile *inputField_;
++ gmx::scoped_cptr<t_inpfile> inpGuard_;
++ warninp_t wi_;
++ gmx::scoped_cptr<struct warninp, free_warning> wiGuard_;
++};
++
++TEST_F(ReadTest, get_eint_ReadsInteger)
++{
++ inputField_[0].value = (char *) "1";
++ ASSERT_EQ(1, get_eint(&numInputs_, &inputField_, "test", 2, wi_));
++ ASSERT_FALSE(warning_errors_exist(wi_));
++}
++
++TEST_F(ReadTest, get_eint_WarnsAboutFloat)
++{
++ inputField_[0].value = (char *) "0.8";
++ get_eint(&numInputs_, &inputField_, "test", 2, wi_);
++ ASSERT_TRUE(warning_errors_exist(wi_));
++}
++
++TEST_F(ReadTest, get_eint_WarnsAboutString)
++{
++ inputField_[0].value = (char *) "hello";
++ get_eint(&numInputs_, &inputField_, "test", 2, wi_);
++ ASSERT_TRUE(warning_errors_exist(wi_));
++}
++
++TEST_F(ReadTest, get_eint64_ReadsInteger)
++{
++ inputField_[0].value = (char *) "1";
++ ASSERT_EQ(1, get_eint64(&numInputs_, &inputField_, "test", 2, wi_));
++ ASSERT_FALSE(warning_errors_exist(wi_));
++}
++
++TEST_F(ReadTest, get_eint64_WarnsAboutFloat)
++{
++ inputField_[0].value = (char *) "0.8";
++ get_eint64(&numInputs_, &inputField_, "test", 2, wi_);
++ ASSERT_TRUE(warning_errors_exist(wi_));
++}
++
++TEST_F(ReadTest, get_eint64_WarnsAboutString)
++{
++ inputField_[0].value = (char *) "hello";
++ get_eint64(&numInputs_, &inputField_, "test", 2, wi_);
++ ASSERT_TRUE(warning_errors_exist(wi_));
++}
++
++TEST_F(ReadTest, get_ereal_ReadsInteger)
++{
++ inputField_[0].value = (char *) "1";
++ ASSERT_EQ(1, get_ereal(&numInputs_, &inputField_, "test", 2, wi_));
++ ASSERT_FALSE(warning_errors_exist(wi_));
++}
++
++TEST_F(ReadTest, get_ereal_ReadsFloat)
++{
++ inputField_[0].value = (char *) "0.8";
++ ASSERT_EQ(0.8, get_ereal(&numInputs_, &inputField_, "test", 2, wi_));
++ ASSERT_FALSE(warning_errors_exist(wi_));
++}
++
++TEST_F(ReadTest, get_ereal_WarnsAboutString)
++{
++ inputField_[0].value = (char *) "hello";
++ get_ereal(&numInputs_, &inputField_, "test", 2, wi_);
++ ASSERT_TRUE(warning_errors_exist(wi_));
++}
++
++} // namespace
++} // namespace
--- /dev/null
- * Copyright (c) 2013,2014,2015, by the GROMACS development team, led by
+/*
+ * 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) 2013,2014,2015,2016, 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 "gmxpre.h"
+
+#include "warninp.h"
+
+#include <cstring>
+
+#include "gromacs/utility/cstringutil.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/smalloc.h"
+
+typedef struct warninp {
+ gmx_bool bAllowWarnings;
+ int nwarn_note;
+ int nwarn_warn;
+ int nwarn_error;
+ int maxwarn;
+ int lineno;
+ char filenm[256];
+} t_warninp;
+
+warninp_t init_warning(gmx_bool bAllowWarnings, int maxwarning)
+{
+ warninp_t wi;
+
+ snew(wi, 1);
+
+ wi->bAllowWarnings = bAllowWarnings;
+ wi->maxwarn = maxwarning;
+ wi->nwarn_note = 0;
+ wi->nwarn_warn = 0;
+ wi->nwarn_error = 0;
+ strcpy(wi->filenm, "unknown");
+ wi->lineno = 0;
+
+ return wi;
+}
+
+void set_warning_line(warninp_t wi, const char *s, int line)
+{
+ if (s != NULL)
+ {
+ std::strcpy(wi->filenm, s);
+ }
+ wi->lineno = line;
+}
+
+int get_warning_line(warninp_t wi)
+{
+ return wi->lineno;
+}
+
+const char *get_warning_file(warninp_t wi)
+{
+ return wi->filenm;
+}
+
+static void low_warning(warninp_t wi, const char *wtype, int n, const char *s)
+{
+#define indent 2
+ char *temp, *temp2;
+ int i;
+
+ if (s == NULL)
+ {
+ s = "Empty error message.";
+ }
+ snew(temp, std::strlen(s)+indent+1);
+ for (i = 0; i < indent; i++)
+ {
+ temp[i] = ' ';
+ }
+ temp[indent] = '\0';
+ std::strcat(temp, s);
+ temp2 = wrap_lines(temp, 78-indent, indent, FALSE);
+ if (std::strlen(wi->filenm) > 0)
+ {
+ if (wi->lineno != -1)
+ {
+ fprintf(stderr, "\n%s %d [file %s, line %d]:\n%s\n\n",
+ wtype, n, wi->filenm, wi->lineno, temp2);
+ }
+ else
+ {
+ fprintf(stderr, "\n%s %d [file %s]:\n%s\n\n",
+ wtype, n, wi->filenm, temp2);
+ }
+ }
+ else
+ {
+ fprintf(stderr, "\n%s %d:\n%s\n\n", wtype, n, temp2);
+ }
+ sfree(temp);
+ sfree(temp2);
+}
+
+void warning(warninp_t wi, const char *s)
+{
+ if (wi->bAllowWarnings)
+ {
+ wi->nwarn_warn++;
+ low_warning(wi, "WARNING", wi->nwarn_warn, s);
+ }
+ else
+ {
+ warning_error(wi, s);
+ }
+}
+
+void warning_note(warninp_t wi, const char *s)
+{
+ wi->nwarn_note++;
+ low_warning(wi, "NOTE", wi->nwarn_note, s);
+}
+
+void warning_error(warninp_t wi, const char *s)
+{
+ wi->nwarn_error++;
+ low_warning(wi, "ERROR", wi->nwarn_error, s);
+}
+
+static void print_warn_count(const char *type, int n)
+{
+ if (n > 0)
+ {
+ fprintf(stderr, "\nThere %s %d %s%s\n",
+ (n == 1) ? "was" : "were", n, type, (n == 1) ? "" : "s");
+ }
+}
+
+void check_warning_error(warninp_t wi, int f_errno, const char *file, int line)
+{
+ if (wi->nwarn_error > 0)
+ {
+ print_warn_count("note", wi->nwarn_note);
+ print_warn_count("warning", wi->nwarn_warn);
+
+ gmx_fatal(f_errno, file, line, "There %s %d error%s in input file(s)",
+ (wi->nwarn_error == 1) ? "was" : "were", wi->nwarn_error,
+ (wi->nwarn_error == 1) ? "" : "s");
+ }
+}
+
++gmx_bool warning_errors_exist(warninp_t wi)
++{
++ return (wi->nwarn_error > 0);
++}
++
+void done_warning(warninp_t wi, int f_errno, const char *file, int line)
+{
+ print_warn_count("note", wi->nwarn_note);
+ print_warn_count("warning", wi->nwarn_warn);
+
+ check_warning_error(wi, f_errno, file, line);
+
+ if (wi->maxwarn >= 0 && wi->nwarn_warn > wi->maxwarn)
+ {
+ gmx_fatal(f_errno, file, line,
+ "Too many warnings (%d).\n"
+ "If you are sure all warnings are harmless, use the -maxwarn option.",
+ wi->nwarn_warn);
+ }
+
++ free_warning(wi);
++}
++
++void free_warning(warninp_t wi)
++{
+ sfree(wi);
+}
+
+void _too_few(warninp_t wi, const char *fn, int line)
+{
+ char buf[STRLEN];
+
+ sprintf(buf,
+ "Too few parameters on line (source file %s, line %d)",
+ fn, line);
+ warning(wi, buf);
+}
+
+void _incorrect_n_param(warninp_t wi, const char *fn, int line)
+{
+ char buf[STRLEN];
+
+ sprintf(buf,
+ "Incorrect number of parameters on line (source file %s, line %d)",
+ fn, line);
+ warning(wi, buf);
+}
--- /dev/null
- * Copyright (c) 2010,2014,2015, by the GROMACS development team, led by
+/*
+ * 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) 2010,2014,2015,2016, 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.
+ */
+#ifndef GMX_FILEIO_WARNINP_H
+#define GMX_FILEIO_WARNINP_H
+
+#include "gromacs/utility/basedefinitions.h"
+
+/* Abstract type for warning bookkeeping */
+typedef struct warninp *warninp_t;
+
+
+warninp_t
+init_warning(gmx_bool bAllowWarnings, int maxwarning);
+/* Initialize the warning data structure.
+ * If bAllowWarnings=FALSE, all warnings (calls to warning()) will be
+ * transformed into errors, calls to warning_note still produce notes.
+ * maxwarning determines the maximum number of warnings that are allowed
+ * for proceeding. When this number is exceeded check_warning_error
+ * and done_warning will generate a fatal error.
+ * bAllowWarnings=TRUE should only be used by programs that have
+ * a -maxwarn command line option.
+ */
+
+void
+set_warning_line(warninp_t wi, const char *fn, int line);
+/* Set filename and linenumber for the warning */
+
+int
+get_warning_line(warninp_t wi);
+/* Get linenumber for the warning */
+
+
+const char *
+get_warning_file(warninp_t wi);
+/* Get filename for the warning */
+
+void
+warning(warninp_t wi, const char *s);
+/* Issue a warning, with the string s. If s == NULL, then warn_buf
+ * will be printed instead. The file and line set by set_warning_line
+ * are printed, nwarn_warn (local) is incremented.
+ * A fatal error will be generated after processing the input
+ * when nwarn_warn is larger than maxwarning passed to init_warning.
+ * So warning should only be called for issues that should be resolved,
+ * otherwise warning_note should be called.
+ */
+
+void
+warning_note(warninp_t wi, const char *s);
+/* Issue a note, with the string s. If s == NULL, then warn_buf
+ * will be printed instead. The file and line set by set_warning_line
+ * are printed, nwarn_note (local) is incremented.
+ * This is for issues which could be a problem for some systems,
+ * but 100% ok for other systems.
+ */
+
+void
+warning_error(warninp_t wi, const char *s);
+/* Issue an error, with the string s. If s == NULL, then warn_buf
+ * will be printed instead. The file and line set by set_warning_line
+ * are printed, nwarn_error (local) is incremented.
+ */
+
++gmx_bool warning_errors_exist(warninp_t wi);
++/* Return whether any error-level warnings were issued to wi. */
++
+void
+check_warning_error(warninp_t wi, int f_errno, const char *file, int line);
+/* When warning_error has been called at least once gmx_fatal is called,
+ * otherwise does nothing.
+ */
+
+void
+done_warning(warninp_t wi, int f_errno, const char *file, int line);
+/* Should be called when finished processing the input file.
+ * Prints the number of notes and warnings
+ * and generates a fatal error when errors were found or too many
+ * warnings were generatesd.
+ * Frees the data structure pointed to by wi.
+ */
+
++void
++free_warning(warninp_t wi);
++/* Frees the data structure pointed to by wi. */
++
+void
+_too_few(warninp_t wi, const char *fn, int line);
+#define too_few(wi) _too_few(wi, __FILE__, __LINE__)
+/* Issue a warning stating 'Too few parameters' */
+
+void
+_incorrect_n_param(warninp_t wi, const char *fn, int line);
+#define incorrect_n_param(wi) _incorrect_n_param(wi, __FILE__, __LINE__)
+/* Issue a warning stating 'Incorrect number of parameters' */
+
+#endif
# The nonbonded directory contains subdirectories that are only
# conditionally built, so we cannot use a GLOB_RECURSE here.
-file(GLOB GMXLIB_SOURCES *.c *.cpp)
-
-# gpu utils + cuda tools module
-if(GMX_GPU)
- if(NOT GMX_USE_OPENCL)
- add_subdirectory(cuda_tools)
- else()
- add_subdirectory(ocl_tools)
- endif()
-endif()
-add_subdirectory(gpu_utils)
+file(GLOB GMXLIB_SOURCES *.cpp)
set(GMXLIB_SOURCES ${GMXLIB_SOURCES} ${NONBONDED_SOURCES} PARENT_SCOPE)
-if(BUILD_TESTING)
- add_subdirectory(tests)
-endif()
+
++# if(BUILD_TESTING)
++# add_subdirectory(tests)
++# endif()
--- /dev/null
- readinp.cpp
+ #
+ # This file is part of the GROMACS molecular simulation package.
+ #
+ # Copyright (c) 2016, 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.
+
+ gmx_add_unit_test(GmxlibTests gmxlib-test
+ )
--- /dev/null
- * Copyright (c) 2013,2014,2015, by the GROMACS development team, led by
+/*
+ * 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.
- int couple_lam0, int couple_lam1)
++ * Copyright (c) 2013,2014,2015,2016, 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 "gmxpre.h"
+
+#include "toppush.h"
+
+#include <ctype.h>
+#include <stdlib.h>
+
+#include <cmath>
+
+#include <algorithm>
+
+#include "gromacs/fileio/warninp.h"
+#include "gromacs/gmxpreprocess/gpp_atomtype.h"
+#include "gromacs/gmxpreprocess/gpp_bond_atomtype.h"
+#include "gromacs/gmxpreprocess/notset.h"
+#include "gromacs/gmxpreprocess/readir.h"
+#include "gromacs/gmxpreprocess/topdirs.h"
+#include "gromacs/gmxpreprocess/toputil.h"
+#include "gromacs/mdtypes/md_enums.h"
+#include "gromacs/topology/ifunc.h"
+#include "gromacs/topology/symtab.h"
+#include "gromacs/utility/cstringutil.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/gmxassert.h"
+#include "gromacs/utility/smalloc.h"
+
+void generate_nbparams(int comb, int ftype, t_params *plist, gpp_atomtype_t atype,
+ warninp_t wi)
+{
+ int i, j, k = -1, nf;
+ int nr, nrfp;
+ real c, bi, bj, ci, cj, ci0, ci1, ci2, cj0, cj1, cj2;
+ char errbuf[256];
+
+ /* Lean mean shortcuts */
+ nr = get_atomtype_ntypes(atype);
+ nrfp = NRFP(ftype);
+ snew(plist->param, nr*nr);
+ plist->nr = nr*nr;
+
+ /* Fill the matrix with force parameters */
+ switch (ftype)
+ {
+ case F_LJ:
+ switch (comb)
+ {
+ case eCOMB_GEOMETRIC:
+ /* Gromos rules */
+ for (i = k = 0; (i < nr); i++)
+ {
+ for (j = 0; (j < nr); j++, k++)
+ {
+ for (nf = 0; (nf < nrfp); nf++)
+ {
+ ci = get_atomtype_nbparam(i, nf, atype);
+ cj = get_atomtype_nbparam(j, nf, atype);
+ c = std::sqrt(ci * cj);
+ plist->param[k].c[nf] = c;
+ }
+ }
+ }
+ break;
+
+ case eCOMB_ARITHMETIC:
+ /* c0 and c1 are sigma and epsilon */
+ for (i = k = 0; (i < nr); i++)
+ {
+ for (j = 0; (j < nr); j++, k++)
+ {
+ ci0 = get_atomtype_nbparam(i, 0, atype);
+ cj0 = get_atomtype_nbparam(j, 0, atype);
+ ci1 = get_atomtype_nbparam(i, 1, atype);
+ cj1 = get_atomtype_nbparam(j, 1, atype);
+ plist->param[k].c[0] = (fabs(ci0) + fabs(cj0))*0.5;
+ /* Negative sigma signals that c6 should be set to zero later,
+ * so we need to propagate that through the combination rules.
+ */
+ if (ci0 < 0 || cj0 < 0)
+ {
+ plist->param[k].c[0] *= -1;
+ }
+ plist->param[k].c[1] = std::sqrt(ci1*cj1);
+ }
+ }
+
+ break;
+ case eCOMB_GEOM_SIG_EPS:
+ /* c0 and c1 are sigma and epsilon */
+ for (i = k = 0; (i < nr); i++)
+ {
+ for (j = 0; (j < nr); j++, k++)
+ {
+ ci0 = get_atomtype_nbparam(i, 0, atype);
+ cj0 = get_atomtype_nbparam(j, 0, atype);
+ ci1 = get_atomtype_nbparam(i, 1, atype);
+ cj1 = get_atomtype_nbparam(j, 1, atype);
+ plist->param[k].c[0] = std::sqrt(fabs(ci0*cj0));
+ /* Negative sigma signals that c6 should be set to zero later,
+ * so we need to propagate that through the combination rules.
+ */
+ if (ci0 < 0 || cj0 < 0)
+ {
+ plist->param[k].c[0] *= -1;
+ }
+ plist->param[k].c[1] = std::sqrt(ci1*cj1);
+ }
+ }
+
+ break;
+ default:
+ gmx_fatal(FARGS, "No such combination rule %d", comb);
+ }
+ if (plist->nr != k)
+ {
+ gmx_incons("Topology processing, generate nb parameters");
+ }
+ break;
+
+ case F_BHAM:
+ /* Buckingham rules */
+ for (i = k = 0; (i < nr); i++)
+ {
+ for (j = 0; (j < nr); j++, k++)
+ {
+ ci0 = get_atomtype_nbparam(i, 0, atype);
+ cj0 = get_atomtype_nbparam(j, 0, atype);
+ ci2 = get_atomtype_nbparam(i, 2, atype);
+ cj2 = get_atomtype_nbparam(j, 2, atype);
+ bi = get_atomtype_nbparam(i, 1, atype);
+ bj = get_atomtype_nbparam(j, 1, atype);
+ plist->param[k].c[0] = std::sqrt(ci0 * cj0);
+ if ((bi == 0) || (bj == 0))
+ {
+ plist->param[k].c[1] = 0;
+ }
+ else
+ {
+ plist->param[k].c[1] = 2.0/(1/bi+1/bj);
+ }
+ plist->param[k].c[2] = std::sqrt(ci2 * cj2);
+ }
+ }
+
+ break;
+ default:
+ sprintf(errbuf, "Invalid nonbonded type %s",
+ interaction_function[ftype].longname);
+ warning_error(wi, errbuf);
+ }
+}
+
+static void realloc_nb_params(gpp_atomtype_t at,
+ t_nbparam ***nbparam, t_nbparam ***pair)
+{
+ /* Add space in the non-bonded parameters matrix */
+ int atnr = get_atomtype_ntypes(at);
+ srenew(*nbparam, atnr);
+ snew((*nbparam)[atnr-1], atnr);
+ if (pair)
+ {
+ srenew(*pair, atnr);
+ snew((*pair)[atnr-1], atnr);
+ }
+}
+
+static void copy_B_from_A(int ftype, double *c)
+{
+ int nrfpA, nrfpB, i;
+
+ nrfpA = NRFPA(ftype);
+ nrfpB = NRFPB(ftype);
+
+ /* Copy the B parameters from the first nrfpB A parameters */
+ for (i = 0; (i < nrfpB); i++)
+ {
+ c[nrfpA+i] = c[i];
+ }
+}
+
+void push_at (t_symtab *symtab, gpp_atomtype_t at, t_bond_atomtype bat,
+ char *line, int nb_funct,
+ t_nbparam ***nbparam, t_nbparam ***pair,
+ warninp_t wi)
+{
+ typedef struct {
+ const char *entry;
+ int ptype;
+ } t_xlate;
+ t_xlate xl[eptNR] = {
+ { "A", eptAtom },
+ { "N", eptNucleus },
+ { "S", eptShell },
+ { "B", eptBond },
+ { "V", eptVSite },
+ };
+
+ int nr, i, nfields, j, pt, nfp0 = -1;
+ int batype_nr, nread;
+ char type[STRLEN], btype[STRLEN], ptype[STRLEN];
+ double m, q;
+ double c[MAXFORCEPARAM];
+ double radius, vol, surftens, gb_radius, S_hct;
+ char tmpfield[12][100]; /* Max 12 fields of width 100 */
+ char errbuf[256];
+ t_atom *atom;
+ t_param *param;
+ int atomnr;
+ gmx_bool have_atomic_number;
+ gmx_bool have_bonded_type;
+
+ snew(atom, 1);
+ snew(param, 1);
+
+ /* First assign input line to temporary array */
+ nfields = sscanf(line, "%s%s%s%s%s%s%s%s%s%s%s%s",
+ tmpfield[0], tmpfield[1], tmpfield[2], tmpfield[3], tmpfield[4], tmpfield[5],
+ tmpfield[6], tmpfield[7], tmpfield[8], tmpfield[9], tmpfield[10], tmpfield[11]);
+
+ /* Comments on optional fields in the atomtypes section:
+ *
+ * The force field format is getting a bit old. For OPLS-AA we needed
+ * to add a special bonded atomtype, and for Gerrit Groenhofs QM/MM stuff
+ * we also needed the atomic numbers.
+ * To avoid making all old or user-generated force fields unusable we
+ * have introduced both these quantities as optional columns, and do some
+ * acrobatics to check whether they are present or not.
+ * This will all look much nicer when we switch to XML... sigh.
+ *
+ * Field 0 (mandatory) is the nonbonded type name. (string)
+ * Field 1 (optional) is the bonded type (string)
+ * Field 2 (optional) is the atomic number (int)
+ * Field 3 (mandatory) is the mass (numerical)
+ * Field 4 (mandatory) is the charge (numerical)
+ * Field 5 (mandatory) is the particle type (single character)
+ * This is followed by a number of nonbonded parameters.
+ *
+ * The safest way to identify the format is the particle type field.
+ *
+ * So, here is what we do:
+ *
+ * A. Read in the first six fields as strings
+ * B. If field 3 (starting from 0) is a single char, we have neither
+ * bonded_type or atomic numbers.
+ * C. If field 5 is a single char we have both.
+ * D. If field 4 is a single char we check field 1. If this begins with
+ * an alphabetical character we have bonded types, otherwise atomic numbers.
+ */
+
+ if (nfields < 6)
+ {
+ too_few(wi);
+ return;
+ }
+
+ if ( (strlen(tmpfield[5]) == 1) && isalpha(tmpfield[5][0]) )
+ {
+ have_bonded_type = TRUE;
+ have_atomic_number = TRUE;
+ }
+ else if ( (strlen(tmpfield[3]) == 1) && isalpha(tmpfield[3][0]) )
+ {
+ have_bonded_type = FALSE;
+ have_atomic_number = FALSE;
+ }
+ else
+ {
+ have_bonded_type = ( isalpha(tmpfield[1][0]) != 0 );
+ have_atomic_number = !have_bonded_type;
+ }
+
+ /* optional fields */
+ surftens = -1;
+ vol = -1;
+ radius = -1;
+ gb_radius = -1;
+ atomnr = -1;
+ S_hct = -1;
+
+ switch (nb_funct)
+ {
+
+ case F_LJ:
+ nfp0 = 2;
+
+ if (have_atomic_number)
+ {
+ if (have_bonded_type)
+ {
+ nread = sscanf(line, "%s%s%d%lf%lf%s%lf%lf%lf%lf%lf%lf",
+ type, btype, &atomnr, &m, &q, ptype, &c[0], &c[1],
+ &radius, &vol, &surftens, &gb_radius);
+ if (nread < 8)
+ {
+ too_few(wi);
+ return;
+ }
+ }
+ else
+ {
+ /* have_atomic_number && !have_bonded_type */
+ nread = sscanf(line, "%s%d%lf%lf%s%lf%lf%lf%lf%lf%lf",
+ type, &atomnr, &m, &q, ptype, &c[0], &c[1],
+ &radius, &vol, &surftens, &gb_radius);
+ if (nread < 7)
+ {
+ too_few(wi);
+ return;
+ }
+ }
+ }
+ else
+ {
+ if (have_bonded_type)
+ {
+ /* !have_atomic_number && have_bonded_type */
+ nread = sscanf(line, "%s%s%lf%lf%s%lf%lf%lf%lf%lf%lf",
+ type, btype, &m, &q, ptype, &c[0], &c[1],
+ &radius, &vol, &surftens, &gb_radius);
+ if (nread < 7)
+ {
+ too_few(wi);
+ return;
+ }
+ }
+ else
+ {
+ /* !have_atomic_number && !have_bonded_type */
+ nread = sscanf(line, "%s%lf%lf%s%lf%lf%lf%lf%lf%lf",
+ type, &m, &q, ptype, &c[0], &c[1],
+ &radius, &vol, &surftens, &gb_radius);
+ if (nread < 6)
+ {
+ too_few(wi);
+ return;
+ }
+ }
+ }
+
+ if (!have_bonded_type)
+ {
+ strcpy(btype, type);
+ }
+
+ if (!have_atomic_number)
+ {
+ atomnr = -1;
+ }
+
+ break;
+
+ case F_BHAM:
+ nfp0 = 3;
+
+ if (have_atomic_number)
+ {
+ if (have_bonded_type)
+ {
+ nread = sscanf(line, "%s%s%d%lf%lf%s%lf%lf%lf%lf%lf%lf%lf",
+ type, btype, &atomnr, &m, &q, ptype, &c[0], &c[1], &c[2],
+ &radius, &vol, &surftens, &gb_radius);
+ if (nread < 9)
+ {
+ too_few(wi);
+ return;
+ }
+ }
+ else
+ {
+ /* have_atomic_number && !have_bonded_type */
+ nread = sscanf(line, "%s%d%lf%lf%s%lf%lf%lf%lf%lf%lf%lf",
+ type, &atomnr, &m, &q, ptype, &c[0], &c[1], &c[2],
+ &radius, &vol, &surftens, &gb_radius);
+ if (nread < 8)
+ {
+ too_few(wi);
+ return;
+ }
+ }
+ }
+ else
+ {
+ if (have_bonded_type)
+ {
+ /* !have_atomic_number && have_bonded_type */
+ nread = sscanf(line, "%s%s%lf%lf%s%lf%lf%lf%lf%lf%lf%lf",
+ type, btype, &m, &q, ptype, &c[0], &c[1], &c[2],
+ &radius, &vol, &surftens, &gb_radius);
+ if (nread < 8)
+ {
+ too_few(wi);
+ return;
+ }
+ }
+ else
+ {
+ /* !have_atomic_number && !have_bonded_type */
+ nread = sscanf(line, "%s%lf%lf%s%lf%lf%lf%lf%lf%lf%lf",
+ type, &m, &q, ptype, &c[0], &c[1], &c[2],
+ &radius, &vol, &surftens, &gb_radius);
+ if (nread < 7)
+ {
+ too_few(wi);
+ return;
+ }
+ }
+ }
+
+ if (!have_bonded_type)
+ {
+ strcpy(btype, type);
+ }
+
+ if (!have_atomic_number)
+ {
+ atomnr = -1;
+ }
+
+ break;
+
+ default:
+ gmx_fatal(FARGS, "Invalid function type %d in push_at %s %d", nb_funct,
+ __FILE__, __LINE__);
+ }
+ for (j = nfp0; (j < MAXFORCEPARAM); j++)
+ {
+ c[j] = 0.0;
+ }
+
+ if (strlen(type) == 1 && isdigit(type[0]))
+ {
+ gmx_fatal(FARGS, "Atom type names can't be single digits.");
+ }
+
+ if (strlen(btype) == 1 && isdigit(btype[0]))
+ {
+ gmx_fatal(FARGS, "Bond atom type names can't be single digits.");
+ }
+
+ /* Hack to read old topologies */
+ if (gmx_strcasecmp(ptype, "D") == 0)
+ {
+ sprintf(ptype, "V");
+ }
+ for (j = 0; (j < eptNR); j++)
+ {
+ if (gmx_strcasecmp(ptype, xl[j].entry) == 0)
+ {
+ break;
+ }
+ }
+ if (j == eptNR)
+ {
+ gmx_fatal(FARGS, "Invalid particle type %s on line %s",
+ ptype, line);
+ }
+ /* cppcheck-suppress arrayIndexOutOfBounds #6329 */
+ pt = xl[j].ptype;
+ if (debug)
+ {
+ fprintf(debug, "ptype: %s\n", ptype_str[pt]);
+ }
+
+ atom->q = q;
+ atom->m = m;
+ atom->ptype = pt;
+ for (i = 0; (i < MAXFORCEPARAM); i++)
+ {
+ param->c[i] = c[i];
+ }
+
+ if ((batype_nr = get_bond_atomtype_type(btype, bat)) == NOTSET)
+ {
+ add_bond_atomtype(bat, symtab, btype);
+ }
+ batype_nr = get_bond_atomtype_type(btype, bat);
+
+ if ((nr = get_atomtype_type(type, at)) != NOTSET)
+ {
+ sprintf(errbuf, "Overriding atomtype %s", type);
+ warning(wi, errbuf);
+ if ((nr = set_atomtype(nr, at, symtab, atom, type, param, batype_nr,
+ radius, vol, surftens, atomnr, gb_radius, S_hct)) == NOTSET)
+ {
+ gmx_fatal(FARGS, "Replacing atomtype %s failed", type);
+ }
+ }
+ else if ((add_atomtype(at, symtab, atom, type, param,
+ batype_nr, radius, vol,
+ surftens, atomnr, gb_radius, S_hct)) == NOTSET)
+ {
+ gmx_fatal(FARGS, "Adding atomtype %s failed", type);
+ }
+ else
+ {
+ /* Add space in the non-bonded parameters matrix */
+ realloc_nb_params(at, nbparam, pair);
+ }
+ sfree(atom);
+ sfree(param);
+}
+
+static void push_bondtype(t_params * bt,
+ t_param * b,
+ int nral,
+ int ftype,
+ gmx_bool bAllowRepeat,
+ char * line,
+ warninp_t wi)
+{
+ int i, j;
+ gmx_bool bTest, bFound, bCont, bId;
+ int nr = bt->nr;
+ int nrfp = NRFP(ftype);
+ char errbuf[256];
+
+ /* If bAllowRepeat is TRUE, we allow multiple entries as long as they
+ are on directly _adjacent_ lines.
+ */
+
+ /* First check if our atomtypes are _identical_ (not reversed) to the previous
+ entry. If they are not identical we search for earlier duplicates. If they are
+ we can skip it, since we already searched for the first line
+ in this group.
+ */
+
+ bFound = FALSE;
+ bCont = FALSE;
+
+ if (bAllowRepeat && nr > 1)
+ {
+ for (j = 0, bCont = TRUE; (j < nral); j++)
+ {
+ bCont = bCont && (b->a[j] == bt->param[nr-2].a[j]);
+ }
+ }
+
+ /* Search for earlier duplicates if this entry was not a continuation
+ from the previous line.
+ */
+ if (!bCont)
+ {
+ bFound = FALSE;
+ for (i = 0; (i < nr); i++)
+ {
+ bTest = TRUE;
+ for (j = 0; (j < nral); j++)
+ {
+ bTest = (bTest && (b->a[j] == bt->param[i].a[j]));
+ }
+ if (!bTest)
+ {
+ bTest = TRUE;
+ for (j = 0; (j < nral); j++)
+ {
+ bTest = (bTest && (b->a[nral-1-j] == bt->param[i].a[j]));
+ }
+ }
+ if (bTest)
+ {
+ if (!bFound)
+ {
+ bId = TRUE;
+ for (j = 0; (j < nrfp); j++)
+ {
+ bId = bId && (bt->param[i].c[j] == b->c[j]);
+ }
+ if (!bId)
+ {
+ sprintf(errbuf, "Overriding %s parameters.%s",
+ interaction_function[ftype].longname,
+ (ftype == F_PDIHS) ?
+ "\nUse dihedraltype 9 to allow several multiplicity terms. Only consecutive lines are combined. Non-consective lines overwrite each other."
+ : "");
+ warning(wi, errbuf);
+ fprintf(stderr, " old: ");
+ for (j = 0; (j < nrfp); j++)
+ {
+ fprintf(stderr, " %g", bt->param[i].c[j]);
+ }
+ fprintf(stderr, " \n new: %s\n\n", line);
+ }
+ }
+ /* Overwrite it! */
+ for (j = 0; (j < nrfp); j++)
+ {
+ bt->param[i].c[j] = b->c[j];
+ }
+ bFound = TRUE;
+ }
+ }
+ }
+ if (!bFound)
+ {
+ /* alloc */
+ pr_alloc (2, bt);
+
+ /* fill the arrays up and down */
+ memcpy(bt->param[bt->nr].c, b->c, sizeof(b->c));
+ memcpy(bt->param[bt->nr].a, b->a, sizeof(b->a));
+ memcpy(bt->param[bt->nr+1].c, b->c, sizeof(b->c));
+
+ /* The definitions of linear angles depend on the order of atoms,
+ * that means that for atoms i-j-k, with certain parameter a, the
+ * corresponding k-j-i angle will have parameter 1-a.
+ */
+ if (ftype == F_LINEAR_ANGLES)
+ {
+ bt->param[bt->nr+1].c[0] = 1-bt->param[bt->nr+1].c[0];
+ bt->param[bt->nr+1].c[2] = 1-bt->param[bt->nr+1].c[2];
+ }
+
+ for (j = 0; (j < nral); j++)
+ {
+ bt->param[bt->nr+1].a[j] = b->a[nral-1-j];
+ }
+
+ bt->nr += 2;
+ }
+}
+
+void push_bt(directive d, t_params bt[], int nral,
+ gpp_atomtype_t at,
+ t_bond_atomtype bat, char *line,
+ warninp_t wi)
+{
+ const char *formal[MAXATOMLIST+1] = {
+ "%s",
+ "%s%s",
+ "%s%s%s",
+ "%s%s%s%s",
+ "%s%s%s%s%s",
+ "%s%s%s%s%s%s",
+ "%s%s%s%s%s%s%s"
+ };
+ const char *formnl[MAXATOMLIST+1] = {
+ "%*s",
+ "%*s%*s",
+ "%*s%*s%*s",
+ "%*s%*s%*s%*s",
+ "%*s%*s%*s%*s%*s",
+ "%*s%*s%*s%*s%*s%*s",
+ "%*s%*s%*s%*s%*s%*s%*s"
+ };
+ const char *formlf = "%lf%lf%lf%lf%lf%lf%lf%lf%lf%lf%lf%lf%lf";
+ int i, ft, ftype, nn, nrfp, nrfpA;
+ char f1[STRLEN];
+ char alc[MAXATOMLIST+1][20];
+ /* One force parameter more, so we can check if we read too many */
+ double c[MAXFORCEPARAM+1];
+ t_param p;
+ char errbuf[256];
+
+ if ((bat && at) || (!bat && !at))
+ {
+ gmx_incons("You should pass either bat or at to push_bt");
+ }
+
+ /* Make format string (nral ints+functype) */
+ if ((nn = sscanf(line, formal[nral],
+ alc[0], alc[1], alc[2], alc[3], alc[4], alc[5])) != nral+1)
+ {
+ sprintf(errbuf, "Not enough atomtypes (%d instead of %d)", nn-1, nral);
+ warning_error(wi, errbuf);
+ return;
+ }
+
+ ft = strtol(alc[nral], NULL, 10);
+ ftype = ifunc_index(d, ft);
+ nrfp = NRFP(ftype);
+ nrfpA = interaction_function[ftype].nrfpA;
+ strcpy(f1, formnl[nral]);
+ strcat(f1, formlf);
+ if ((nn = sscanf(line, f1, &c[0], &c[1], &c[2], &c[3], &c[4], &c[5], &c[6], &c[7], &c[8], &c[9], &c[10], &c[11], &c[12]))
+ != nrfp)
+ {
+ if (nn == nrfpA)
+ {
+ /* Copy the B-state from the A-state */
+ copy_B_from_A(ftype, c);
+ }
+ else
+ {
+ if (nn < nrfpA)
+ {
+ warning_error(wi, "Not enough parameters");
+ }
+ else if (nn > nrfpA && nn < nrfp)
+ {
+ warning_error(wi, "Too many parameters or not enough parameters for topology B");
+ }
+ else if (nn > nrfp)
+ {
+ warning_error(wi, "Too many parameters");
+ }
+ for (i = nn; (i < nrfp); i++)
+ {
+ c[i] = 0.0;
+ }
+ }
+ }
+ for (i = 0; (i < nral); i++)
+ {
+ if (at && ((p.a[i] = get_atomtype_type(alc[i], at)) == NOTSET))
+ {
+ gmx_fatal(FARGS, "Unknown atomtype %s\n", alc[i]);
+ }
+ else if (bat && ((p.a[i] = get_bond_atomtype_type(alc[i], bat)) == NOTSET))
+ {
+ gmx_fatal(FARGS, "Unknown bond_atomtype %s\n", alc[i]);
+ }
+ }
+ for (i = 0; (i < nrfp); i++)
+ {
+ p.c[i] = c[i];
+ }
+ push_bondtype (&(bt[ftype]), &p, nral, ftype, FALSE, line, wi);
+}
+
+
+void push_dihedraltype(directive d, t_params bt[],
+ t_bond_atomtype bat, char *line,
+ warninp_t wi)
+{
+ const char *formal[MAXATOMLIST+1] = {
+ "%s",
+ "%s%s",
+ "%s%s%s",
+ "%s%s%s%s",
+ "%s%s%s%s%s",
+ "%s%s%s%s%s%s",
+ "%s%s%s%s%s%s%s"
+ };
+ const char *formnl[MAXATOMLIST+1] = {
+ "%*s",
+ "%*s%*s",
+ "%*s%*s%*s",
+ "%*s%*s%*s%*s",
+ "%*s%*s%*s%*s%*s",
+ "%*s%*s%*s%*s%*s%*s",
+ "%*s%*s%*s%*s%*s%*s%*s"
+ };
+ const char *formlf[MAXFORCEPARAM] = {
+ "%lf",
+ "%lf%lf",
+ "%lf%lf%lf",
+ "%lf%lf%lf%lf",
+ "%lf%lf%lf%lf%lf",
+ "%lf%lf%lf%lf%lf%lf",
+ "%lf%lf%lf%lf%lf%lf%lf",
+ "%lf%lf%lf%lf%lf%lf%lf%lf",
+ "%lf%lf%lf%lf%lf%lf%lf%lf%lf",
+ "%lf%lf%lf%lf%lf%lf%lf%lf%lf%lf",
+ "%lf%lf%lf%lf%lf%lf%lf%lf%lf%lf%lf",
+ "%lf%lf%lf%lf%lf%lf%lf%lf%lf%lf%lf%lf",
+ };
+ int i, ft, ftype, nn, nrfp, nrfpA, nral;
+ char f1[STRLEN];
+ char alc[MAXATOMLIST+1][20];
+ double c[MAXFORCEPARAM];
+ t_param p;
+ gmx_bool bAllowRepeat;
+ char errbuf[256];
+
+ /* This routine accepts dihedraltypes defined from either 2 or 4 atoms.
+ *
+ * We first check for 2 atoms with the 3th column being an integer
+ * defining the type. If this isn't the case, we try it with 4 atoms
+ * and the 5th column defining the dihedral type.
+ */
+ nn = sscanf(line, formal[4], alc[0], alc[1], alc[2], alc[3], alc[4]);
+ if (nn >= 3 && strlen(alc[2]) == 1 && isdigit(alc[2][0]))
+ {
+ nral = 2;
+ ft = strtol(alc[nral], NULL, 10);
+ /* Move atom types around a bit and use 'X' for wildcard atoms
+ * to create a 4-atom dihedral definition with arbitrary atoms in
+ * position 1 and 4.
+ */
+ if (alc[2][0] == '2')
+ {
+ /* improper - the two atomtypes are 1,4. Use wildcards for 2,3 */
+ strcpy(alc[3], alc[1]);
+ sprintf(alc[2], "X");
+ sprintf(alc[1], "X");
+ /* alc[0] stays put */
+ }
+ else
+ {
+ /* proper - the two atomtypes are 2,3. Use wildcards for 1,4 */
+ sprintf(alc[3], "X");
+ strcpy(alc[2], alc[1]);
+ strcpy(alc[1], alc[0]);
+ sprintf(alc[0], "X");
+ }
+ }
+ else if (nn == 5 && strlen(alc[4]) == 1 && isdigit(alc[4][0]))
+ {
+ nral = 4;
+ ft = strtol(alc[nral], NULL, 10);
+ }
+ else
+ {
+ sprintf(errbuf, "Incorrect number of atomtypes for dihedral (%d instead of 2 or 4)", nn-1);
+ warning_error(wi, errbuf);
+ return;
+ }
+
+ if (ft == 9)
+ {
+ /* Previously, we have always overwritten parameters if e.g. a torsion
+ with the same atomtypes occurs on multiple lines. However, CHARMM and
+ some other force fields specify multiple dihedrals over some bonds,
+ including cosines with multiplicity 6 and somethimes even higher.
+ Thus, they cannot be represented with Ryckaert-Bellemans terms.
+ To add support for these force fields, Dihedral type 9 is identical to
+ normal proper dihedrals, but repeated entries are allowed.
+ */
+ bAllowRepeat = TRUE;
+ ft = 1;
+ }
+ else
+ {
+ bAllowRepeat = FALSE;
+ }
+
+
+ ftype = ifunc_index(d, ft);
+ nrfp = NRFP(ftype);
+ nrfpA = interaction_function[ftype].nrfpA;
+
+ strcpy(f1, formnl[nral]);
+ strcat(f1, formlf[nrfp-1]);
+
+ /* Check number of parameters given */
+ if ((nn = sscanf(line, f1, &c[0], &c[1], &c[2], &c[3], &c[4], &c[5], &c[6], &c[7], &c[8], &c[9], &c[10], &c[11]))
+ != nrfp)
+ {
+ if (nn == nrfpA)
+ {
+ /* Copy the B-state from the A-state */
+ copy_B_from_A(ftype, c);
+ }
+ else
+ {
+ if (nn < nrfpA)
+ {
+ warning_error(wi, "Not enough parameters");
+ }
+ else if (nn > nrfpA && nn < nrfp)
+ {
+ warning_error(wi, "Too many parameters or not enough parameters for topology B");
+ }
+ else if (nn > nrfp)
+ {
+ warning_error(wi, "Too many parameters");
+ }
+ for (i = nn; (i < nrfp); i++)
+ {
+ c[i] = 0.0;
+ }
+ }
+ }
+
+ for (i = 0; (i < 4); i++)
+ {
+ if (!strcmp(alc[i], "X"))
+ {
+ p.a[i] = -1;
+ }
+ else
+ {
+ if ((p.a[i] = get_bond_atomtype_type(alc[i], bat)) == NOTSET)
+ {
+ gmx_fatal(FARGS, "Unknown bond_atomtype %s", alc[i]);
+ }
+ }
+ }
+ for (i = 0; (i < nrfp); i++)
+ {
+ p.c[i] = c[i];
+ }
+ /* Always use 4 atoms here, since we created two wildcard atoms
+ * if there wasn't of them 4 already.
+ */
+ push_bondtype (&(bt[ftype]), &p, 4, ftype, bAllowRepeat, line, wi);
+}
+
+
+void push_nbt(directive d, t_nbparam **nbt, gpp_atomtype_t atype,
+ char *pline, int nb_funct,
+ warninp_t wi)
+{
+ /* swap the atoms */
+ const char *form3 = "%*s%*s%*s%lf%lf%lf";
+ const char *form4 = "%*s%*s%*s%lf%lf%lf%lf";
+ const char *form5 = "%*s%*s%*s%lf%lf%lf%lf%lf";
+ char a0[80], a1[80];
+ int i, f, n, ftype, nrfp;
+ double c[4], dum;
+ real cr[4];
+ int ai, aj;
+ t_nbparam *nbp;
+ gmx_bool bId;
+ char errbuf[256];
+
+ if (sscanf (pline, "%s%s%d", a0, a1, &f) != 3)
+ {
+ too_few(wi);
+ return;
+ }
+
+ ftype = ifunc_index(d, f);
+
+ if (ftype != nb_funct)
+ {
+ sprintf(errbuf, "Trying to add %s while the default nonbond type is %s",
+ interaction_function[ftype].longname,
+ interaction_function[nb_funct].longname);
+ warning_error(wi, errbuf);
+ return;
+ }
+
+ /* Get the force parameters */
+ nrfp = NRFP(ftype);
+ if (ftype == F_LJ14)
+ {
+ n = sscanf(pline, form4, &c[0], &c[1], &c[2], &c[3]);
+ if (n < 2)
+ {
+ too_few(wi);
+ return;
+ }
+ /* When the B topology parameters are not set,
+ * copy them from topology A
+ */
+ GMX_ASSERT(nrfp <= 4, "LJ-14 cannot have more than 4 parameters");
+ for (i = n; i < nrfp; i++)
+ {
+ c[i] = c[i-2];
+ }
+ }
+ else if (ftype == F_LJC14_Q)
+ {
+ n = sscanf(pline, form5, &c[0], &c[1], &c[2], &c[3], &dum);
+ if (n != 4)
+ {
+ incorrect_n_param(wi);
+ return;
+ }
+ }
+ else if (nrfp == 2)
+ {
+ if (sscanf(pline, form3, &c[0], &c[1], &dum) != 2)
+ {
+ incorrect_n_param(wi);
+ return;
+ }
+ }
+ else if (nrfp == 3)
+ {
+ if (sscanf(pline, form4, &c[0], &c[1], &c[2], &dum) != 3)
+ {
+ incorrect_n_param(wi);
+ return;
+ }
+ }
+ else
+ {
+ gmx_fatal(FARGS, "Number of force parameters for nonbonded interactions is %d"
+ " in file %s, line %d", nrfp, __FILE__, __LINE__);
+ }
+ for (i = 0; (i < nrfp); i++)
+ {
+ cr[i] = c[i];
+ }
+
+ /* Put the parameters in the matrix */
+ if ((ai = get_atomtype_type (a0, atype)) == NOTSET)
+ {
+ gmx_fatal(FARGS, "Atomtype %s not found", a0);
+ }
+ if ((aj = get_atomtype_type (a1, atype)) == NOTSET)
+ {
+ gmx_fatal(FARGS, "Atomtype %s not found", a1);
+ }
+ nbp = &(nbt[std::max(ai, aj)][std::min(ai, aj)]);
+
+ if (nbp->bSet)
+ {
+ bId = TRUE;
+ for (i = 0; i < nrfp; i++)
+ {
+ bId = bId && (nbp->c[i] == cr[i]);
+ }
+ if (!bId)
+ {
+ sprintf(errbuf, "Overriding non-bonded parameters,");
+ warning(wi, errbuf);
+ fprintf(stderr, " old:");
+ for (i = 0; i < nrfp; i++)
+ {
+ fprintf(stderr, " %g", nbp->c[i]);
+ }
+ fprintf(stderr, " new\n%s\n", pline);
+ }
+ }
+ nbp->bSet = TRUE;
+ for (i = 0; i < nrfp; i++)
+ {
+ nbp->c[i] = cr[i];
+ }
+}
+
+void
+push_gb_params (gpp_atomtype_t at, char *line,
+ warninp_t wi)
+{
+ int atype;
+ double radius, vol, surftens, gb_radius, S_hct;
+ char atypename[STRLEN];
+ char errbuf[STRLEN];
+
+ if ( (sscanf(line, "%s%lf%lf%lf%lf%lf", atypename, &radius, &vol, &surftens, &gb_radius, &S_hct)) != 6)
+ {
+ sprintf(errbuf, "Too few gb parameters for type %s\n", atypename);
+ warning(wi, errbuf);
+ }
+
+ /* Search for atomtype */
+ atype = get_atomtype_type(atypename, at);
+
+ if (atype == NOTSET)
+ {
+ printf("Couldn't find topology match for atomtype %s\n", atypename);
+ abort();
+ }
+
+ set_atomtype_gbparam(at, atype, radius, vol, surftens, gb_radius, S_hct);
+}
+
+void
+push_cmaptype(directive d, t_params bt[], int nral, gpp_atomtype_t at,
+ t_bond_atomtype bat, char *line,
+ warninp_t wi)
+{
+ const char *formal = "%s%s%s%s%s%s%s%s";
+
+ int i, ft, ftype, nn, nrfp, nrfpA, nrfpB;
+ int start;
+ int nxcmap, nycmap, ncmap, read_cmap, sl, nct;
+ char s[20], alc[MAXATOMLIST+2][20];
+ t_param p;
+ char errbuf[256];
+
+ /* Keep the compiler happy */
+ read_cmap = 0;
+ start = 0;
+
+ if ((nn = sscanf(line, formal, alc[0], alc[1], alc[2], alc[3], alc[4], alc[5], alc[6], alc[7])) != nral+3)
+ {
+ sprintf(errbuf, "Incorrect number of atomtypes for cmap (%d instead of 5)", nn-1);
+ warning_error(wi, errbuf);
+ return;
+ }
+
+ /* Compute an offset for each line where the cmap parameters start
+ * ie. where the atom types and grid spacing information ends
+ */
+ for (i = 0; i < nn; i++)
+ {
+ start += (int)strlen(alc[i]);
+ }
+
+ /* There are nn-1 spaces between the atom types and the grid spacing info in the cmap.itp file */
+ /* start is the position on the line where we start to read the actual cmap grid data from the itp file */
+ start = start + nn -1;
+
+ ft = strtol(alc[nral], NULL, 10);
+ nxcmap = strtol(alc[nral+1], NULL, 10);
+ nycmap = strtol(alc[nral+2], NULL, 10);
+
+ /* Check for equal grid spacing in x and y dims */
+ if (nxcmap != nycmap)
+ {
+ gmx_fatal(FARGS, "Not the same grid spacing in x and y for cmap grid: x=%d, y=%d", nxcmap, nycmap);
+ }
+
+ ncmap = nxcmap*nycmap;
+ ftype = ifunc_index(d, ft);
+ nrfpA = strtol(alc[6], NULL, 10)*strtol(alc[6], NULL, 10);
+ nrfpB = strtol(alc[7], NULL, 10)*strtol(alc[7], NULL, 10);
+ nrfp = nrfpA+nrfpB;
+
+ /* Allocate memory for the CMAP grid */
+ bt[F_CMAP].ncmap += nrfp;
+ srenew(bt[F_CMAP].cmap, bt[F_CMAP].ncmap);
+
+ /* Read in CMAP parameters */
+ sl = 0;
+ for (i = 0; i < ncmap; i++)
+ {
+ while (isspace(*(line+start+sl)))
+ {
+ sl++;
+ }
+ nn = sscanf(line+start+sl, " %s ", s);
+ sl += strlen(s);
+ bt[F_CMAP].cmap[i+(bt[F_CMAP].ncmap)-nrfp] = strtod(s, NULL);
+
+ if (nn == 1)
+ {
+ read_cmap++;
+ }
+ else
+ {
+ gmx_fatal(FARGS, "Error in reading cmap parameter for angle %s %s %s %s %s", alc[0], alc[1], alc[2], alc[3], alc[4]);
+ }
+
+ }
+
+ /* Check do that we got the number of parameters we expected */
+ if (read_cmap == nrfpA)
+ {
+ for (i = 0; i < ncmap; i++)
+ {
+ bt[F_CMAP].cmap[i+ncmap] = bt[F_CMAP].cmap[i];
+ }
+ }
+ else
+ {
+ if (read_cmap < nrfpA)
+ {
+ warning_error(wi, "Not enough cmap parameters");
+ }
+ else if (read_cmap > nrfpA && read_cmap < nrfp)
+ {
+ warning_error(wi, "Too many cmap parameters or not enough parameters for topology B");
+ }
+ else if (read_cmap > nrfp)
+ {
+ warning_error(wi, "Too many cmap parameters");
+ }
+ }
+
+
+ /* Set grid spacing and the number of grids (we assume these numbers to be the same for all grids
+ * so we can safely assign them each time
+ */
+ bt[F_CMAP].grid_spacing = nxcmap; /* Or nycmap, they need to be equal */
+ bt[F_CMAP].nc = bt[F_CMAP].nc + 1; /* Since we are incrementing here, we need to subtract later, see (*****) */
+ nct = (nral+1) * bt[F_CMAP].nc;
+
+ /* Allocate memory for the cmap_types information */
+ srenew(bt[F_CMAP].cmap_types, nct);
+
+ for (i = 0; (i < nral); i++)
+ {
+ if (at && ((p.a[i] = get_bond_atomtype_type(alc[i], bat)) == NOTSET))
+ {
+ gmx_fatal(FARGS, "Unknown atomtype %s\n", alc[i]);
+ }
+ else if (bat && ((p.a[i] = get_bond_atomtype_type(alc[i], bat)) == NOTSET))
+ {
+ gmx_fatal(FARGS, "Unknown bond_atomtype %s\n", alc[i]);
+ }
+
+ /* Assign a grid number to each cmap_type */
+ bt[F_CMAP].cmap_types[bt[F_CMAP].nct++] = get_bond_atomtype_type(alc[i], bat);
+ }
+
+ /* Assign a type number to this cmap */
+ bt[F_CMAP].cmap_types[bt[F_CMAP].nct++] = bt[F_CMAP].nc-1; /* Since we inremented earlier, we need to subtrac here, to get the types right (****) */
+
+ /* Check for the correct number of atoms (again) */
+ if (bt[F_CMAP].nct != nct)
+ {
+ gmx_fatal(FARGS, "Incorrect number of atom types (%d) in cmap type %d\n", nct, bt[F_CMAP].nc);
+ }
+
+ /* Is this correct?? */
+ for (i = 0; i < MAXFORCEPARAM; i++)
+ {
+ p.c[i] = NOTSET;
+ }
+
+ /* Push the bond to the bondlist */
+ push_bondtype (&(bt[ftype]), &p, nral, ftype, FALSE, line, wi);
+}
+
+
+static void push_atom_now(t_symtab *symtab, t_atoms *at, int atomnr,
+ int atomicnumber,
+ int type, char *ctype, int ptype,
+ char *resnumberic,
+ char *resname, char *name, real m0, real q0,
+ int typeB, char *ctypeB, real mB, real qB)
+{
+ int j, resind = 0, resnr;
+ unsigned char ric;
+ int nr = at->nr;
+
+ if (((nr == 0) && (atomnr != 1)) || (nr && (atomnr != at->nr+1)))
+ {
+ gmx_fatal(FARGS, "Atoms in the .top are not numbered consecutively from 1 (rather, atomnr = %d, while at->nr = %d)", atomnr, at->nr);
+ }
+
+ j = strlen(resnumberic) - 1;
+ if (isdigit(resnumberic[j]))
+ {
+ ric = ' ';
+ }
+ else
+ {
+ ric = resnumberic[j];
+ if (j == 0 || !isdigit(resnumberic[j-1]))
+ {
+ gmx_fatal(FARGS, "Invalid residue number '%s' for atom %d",
+ resnumberic, atomnr);
+ }
+ }
+ resnr = strtol(resnumberic, NULL, 10);
+
+ if (nr > 0)
+ {
+ resind = at->atom[nr-1].resind;
+ }
+ if (nr == 0 || strcmp(resname, *at->resinfo[resind].name) != 0 ||
+ resnr != at->resinfo[resind].nr ||
+ ric != at->resinfo[resind].ic)
+ {
+ if (nr == 0)
+ {
+ resind = 0;
+ }
+ else
+ {
+ resind++;
+ }
+ at->nres = resind + 1;
+ srenew(at->resinfo, at->nres);
+ at->resinfo[resind].name = put_symtab(symtab, resname);
+ at->resinfo[resind].nr = resnr;
+ at->resinfo[resind].ic = ric;
+ }
+ else
+ {
+ resind = at->atom[at->nr-1].resind;
+ }
+
+ /* New atom instance
+ * get new space for arrays
+ */
+ srenew(at->atom, nr+1);
+ srenew(at->atomname, nr+1);
+ srenew(at->atomtype, nr+1);
+ srenew(at->atomtypeB, nr+1);
+
+ /* fill the list */
+ at->atom[nr].type = type;
+ at->atom[nr].ptype = ptype;
+ at->atom[nr].q = q0;
+ at->atom[nr].m = m0;
+ at->atom[nr].typeB = typeB;
+ at->atom[nr].qB = qB;
+ at->atom[nr].mB = mB;
+
+ at->atom[nr].resind = resind;
+ at->atom[nr].atomnumber = atomicnumber;
+ at->atomname[nr] = put_symtab(symtab, name);
+ at->atomtype[nr] = put_symtab(symtab, ctype);
+ at->atomtypeB[nr] = put_symtab(symtab, ctypeB);
+ at->nr++;
+}
+
+void push_cg(t_block *block, int *lastindex, int index, int a)
+{
+ if (debug)
+ {
+ fprintf (debug, "Index %d, Atom %d\n", index, a);
+ }
+
+ if (((block->nr) && (*lastindex != index)) || (!block->nr))
+ {
+ /* add a new block */
+ block->nr++;
+ srenew(block->index, block->nr+1);
+ }
+ block->index[block->nr] = a + 1;
+ *lastindex = index;
+}
+
+void push_atom(t_symtab *symtab, t_block *cgs,
+ t_atoms *at, gpp_atomtype_t atype, char *line, int *lastcg,
+ warninp_t wi)
+{
+ int nr, ptype;
+ int cgnumber, atomnr, type, typeB, nscan;
+ char id[STRLEN], ctype[STRLEN], ctypeB[STRLEN],
+ resnumberic[STRLEN], resname[STRLEN], name[STRLEN], check[STRLEN];
+ double m, q, mb, qb;
+ real m0, q0, mB, qB;
+
+ /* Make a shortcut for writing in this molecule */
+ nr = at->nr;
+
+ /* Fixed parameters */
+ if (sscanf(line, "%s%s%s%s%s%d",
+ id, ctype, resnumberic, resname, name, &cgnumber) != 6)
+ {
+ too_few(wi);
+ return;
+ }
+ sscanf(id, "%d", &atomnr);
+ if ((type = get_atomtype_type(ctype, atype)) == NOTSET)
+ {
+ gmx_fatal(FARGS, "Atomtype %s not found", ctype);
+ }
+ ptype = get_atomtype_ptype(type, atype);
+
+ /* Set default from type */
+ q0 = get_atomtype_qA(type, atype);
+ m0 = get_atomtype_massA(type, atype);
+ typeB = type;
+ qB = q0;
+ mB = m0;
+
+ /* Optional parameters */
+ nscan = sscanf(line, "%*s%*s%*s%*s%*s%*s%lf%lf%s%lf%lf%s",
+ &q, &m, ctypeB, &qb, &mb, check);
+
+ /* Nasty switch that falls thru all the way down! */
+ if (nscan > 0)
+ {
+ q0 = qB = q;
+ if (nscan > 1)
+ {
+ m0 = mB = m;
+ if (nscan > 2)
+ {
+ if ((typeB = get_atomtype_type(ctypeB, atype)) == NOTSET)
+ {
+ gmx_fatal(FARGS, "Atomtype %s not found", ctypeB);
+ }
+ qB = get_atomtype_qA(typeB, atype);
+ mB = get_atomtype_massA(typeB, atype);
+ if (nscan > 3)
+ {
+ qB = qb;
+ if (nscan > 4)
+ {
+ mB = mb;
+ if (nscan > 5)
+ {
+ warning_error(wi, "Too many parameters");
+ }
+ }
+ }
+ }
+ }
+ }
+ if (debug)
+ {
+ fprintf(debug, "mB=%g, qB=%g, typeB=%d\n", mB, qB, typeB);
+ }
+
+ push_cg(cgs, lastcg, cgnumber, nr);
+
+ push_atom_now(symtab, at, atomnr, get_atomtype_atomnumber(type, atype),
+ type, ctype, ptype, resnumberic,
+ resname, name, m0, q0, typeB,
+ typeB == type ? ctype : ctypeB, mB, qB);
+}
+
+void push_molt(t_symtab *symtab, int *nmol, t_molinfo **mol, char *line,
+ warninp_t wi)
+{
+ char type[STRLEN];
+ int nrexcl, i;
+ t_molinfo *newmol;
+
+ if ((sscanf(line, "%s%d", type, &nrexcl)) != 2)
+ {
+ warning_error(wi, "Expected a molecule type name and nrexcl");
+ }
+
+ /* Test if this moleculetype overwrites another */
+ i = 0;
+ while (i < *nmol)
+ {
+ if (strcmp(*((*mol)[i].name), type) == 0)
+ {
+ gmx_fatal(FARGS, "moleculetype %s is redefined", type);
+ }
+ i++;
+ }
+
+ (*nmol)++;
+ srenew(*mol, *nmol);
+ newmol = &((*mol)[*nmol-1]);
+ init_molinfo(newmol);
+
+ /* Fill in the values */
+ newmol->name = put_symtab(symtab, type);
+ newmol->nrexcl = nrexcl;
+ newmol->excl_set = FALSE;
+}
+
+static gmx_bool default_nb_params(int ftype, t_params bt[], t_atoms *at,
+ t_param *p, int c_start, gmx_bool bB, gmx_bool bGenPairs)
+{
+ int i, j, ti, tj, ntype;
+ gmx_bool bFound;
+ t_param *pi = NULL;
+ int nr = bt[ftype].nr;
+ int nral = NRAL(ftype);
+ int nrfp = interaction_function[ftype].nrfpA;
+ int nrfpB = interaction_function[ftype].nrfpB;
+
+ if ((!bB && nrfp == 0) || (bB && nrfpB == 0))
+ {
+ return TRUE;
+ }
+
+ bFound = FALSE;
+ if (bGenPairs)
+ {
+ /* First test the generated-pair position to save
+ * time when we have 1000*1000 entries for e.g. OPLS...
+ */
+ ntype = static_cast<int>(std::sqrt(static_cast<double>(nr)));
+ GMX_ASSERT(ntype * ntype == nr, "Number of pairs of generated non-bonded parameters should be a perfect square");
+ if (bB)
+ {
+ ti = at->atom[p->a[0]].typeB;
+ tj = at->atom[p->a[1]].typeB;
+ }
+ else
+ {
+ ti = at->atom[p->a[0]].type;
+ tj = at->atom[p->a[1]].type;
+ }
+ pi = &(bt[ftype].param[ntype*ti+tj]);
+ bFound = ((ti == pi->a[0]) && (tj == pi->a[1]));
+ }
+
+ /* Search explicitly if we didnt find it */
+ if (!bFound)
+ {
+ for (i = 0; ((i < nr) && !bFound); i++)
+ {
+ pi = &(bt[ftype].param[i]);
+ if (bB)
+ {
+ for (j = 0; ((j < nral) &&
+ (at->atom[p->a[j]].typeB == pi->a[j])); j++)
+ {
+ ;
+ }
+ }
+ else
+ {
+ for (j = 0; ((j < nral) &&
+ (at->atom[p->a[j]].type == pi->a[j])); j++)
+ {
+ ;
+ }
+ }
+ bFound = (j == nral);
+ }
+ }
+
+ if (bFound)
+ {
+ if (bB)
+ {
+ if (nrfp+nrfpB > MAXFORCEPARAM)
+ {
+ gmx_incons("Too many force parameters");
+ }
+ for (j = c_start; (j < nrfpB); j++)
+ {
+ p->c[nrfp+j] = pi->c[j];
+ }
+ }
+ else
+ {
+ for (j = c_start; (j < nrfp); j++)
+ {
+ p->c[j] = pi->c[j];
+ }
+ }
+ }
+ else
+ {
+ for (j = c_start; (j < nrfp); j++)
+ {
+ p->c[j] = 0.0;
+ }
+ }
+ return bFound;
+}
+
+static gmx_bool default_cmap_params(t_params bondtype[],
+ t_atoms *at, gpp_atomtype_t atype,
+ t_param *p, gmx_bool bB,
+ int *cmap_type, int *nparam_def)
+{
+ int i, nparam_found;
+ int ct;
+ gmx_bool bFound = FALSE;
+
+ nparam_found = 0;
+ ct = 0;
+
+ /* Match the current cmap angle against the list of cmap_types */
+ for (i = 0; i < bondtype[F_CMAP].nct && !bFound; i += 6)
+ {
+ if (bB)
+ {
+
+ }
+ else
+ {
+ if (
+ (get_atomtype_batype(at->atom[p->a[0]].type, atype) == bondtype[F_CMAP].cmap_types[i]) &&
+ (get_atomtype_batype(at->atom[p->a[1]].type, atype) == bondtype[F_CMAP].cmap_types[i+1]) &&
+ (get_atomtype_batype(at->atom[p->a[2]].type, atype) == bondtype[F_CMAP].cmap_types[i+2]) &&
+ (get_atomtype_batype(at->atom[p->a[3]].type, atype) == bondtype[F_CMAP].cmap_types[i+3]) &&
+ (get_atomtype_batype(at->atom[p->a[4]].type, atype) == bondtype[F_CMAP].cmap_types[i+4]))
+ {
+ /* Found cmap torsion */
+ bFound = TRUE;
+ ct = bondtype[F_CMAP].cmap_types[i+5];
+ nparam_found = 1;
+ }
+ }
+ }
+
+ /* If we did not find a matching type for this cmap torsion */
+ if (!bFound)
+ {
+ gmx_fatal(FARGS, "Unknown cmap torsion between atoms %d %d %d %d %d\n",
+ p->a[0]+1, p->a[1]+1, p->a[2]+1, p->a[3]+1, p->a[4]+1);
+ }
+
+ *nparam_def = nparam_found;
+ *cmap_type = ct;
+
+ return bFound;
+}
+
+static gmx_bool default_params(int ftype, t_params bt[],
+ t_atoms *at, gpp_atomtype_t atype,
+ t_param *p, gmx_bool bB,
+ t_param **param_def,
+ int *nparam_def)
+{
+ int i, j, nparam_found;
+ gmx_bool bFound, bSame;
+ t_param *pi = NULL;
+ t_param *pj = NULL;
+ int nr = bt[ftype].nr;
+ int nral = NRAL(ftype);
+ int nrfpA = interaction_function[ftype].nrfpA;
+ int nrfpB = interaction_function[ftype].nrfpB;
+
+ if ((!bB && nrfpA == 0) || (bB && nrfpB == 0))
+ {
+ return TRUE;
+ }
+
+
+ /* We allow wildcards now. The first type (with or without wildcards) that
+ * fits is used, so you should probably put the wildcarded bondtypes
+ * at the end of each section.
+ */
+ bFound = FALSE;
+ nparam_found = 0;
+ /* OPLS uses 1000s of dihedraltypes, so in order to speed up the scanning we have a
+ * special case for this. Check for B state outside loop to speed it up.
+ */
+ if (ftype == F_PDIHS || ftype == F_RBDIHS || ftype == F_IDIHS || ftype == F_PIDIHS)
+ {
+ if (bB)
+ {
+ for (i = 0; ((i < nr) && !bFound); i++)
+ {
+ pi = &(bt[ftype].param[i]);
+ bFound =
+ (
+ ((pi->ai() == -1) || (get_atomtype_batype(at->atom[p->ai()].typeB, atype) == pi->ai())) &&
+ ((pi->aj() == -1) || (get_atomtype_batype(at->atom[p->aj()].typeB, atype) == pi->aj())) &&
+ ((pi->ak() == -1) || (get_atomtype_batype(at->atom[p->ak()].typeB, atype) == pi->ak())) &&
+ ((pi->al() == -1) || (get_atomtype_batype(at->atom[p->al()].typeB, atype) == pi->al()))
+ );
+ }
+ }
+ else
+ {
+ /* State A */
+ for (i = 0; ((i < nr) && !bFound); i++)
+ {
+ pi = &(bt[ftype].param[i]);
+ bFound =
+ (
+ ((pi->ai() == -1) || (get_atomtype_batype(at->atom[p->ai()].type, atype) == pi->ai())) &&
+ ((pi->aj() == -1) || (get_atomtype_batype(at->atom[p->aj()].type, atype) == pi->aj())) &&
+ ((pi->ak() == -1) || (get_atomtype_batype(at->atom[p->ak()].type, atype) == pi->ak())) &&
+ ((pi->al() == -1) || (get_atomtype_batype(at->atom[p->al()].type, atype) == pi->al()))
+ );
+ }
+ }
+ /* Find additional matches for this dihedral - necessary for ftype==9 which is used e.g. for charmm.
+ * The rules in that case is that additional matches HAVE to be on adjacent lines!
+ */
+ if (bFound == TRUE)
+ {
+ nparam_found++;
+ bSame = TRUE;
+ /* Continue from current i value */
+ for (j = i+1; j < nr && bSame; j += 2)
+ {
+ pj = &(bt[ftype].param[j]);
+ bSame = (pi->ai() == pj->ai() && pi->aj() == pj->aj() && pi->ak() == pj->ak() && pi->al() == pj->al());
+ if (bSame)
+ {
+ nparam_found++;
+ }
+ /* nparam_found will be increased as long as the numbers match */
+ }
+ }
+ }
+ else /* Not a dihedral */
+ {
+ for (i = 0; ((i < nr) && !bFound); i++)
+ {
+ pi = &(bt[ftype].param[i]);
+ if (bB)
+ {
+ for (j = 0; ((j < nral) &&
+ (get_atomtype_batype(at->atom[p->a[j]].typeB, atype) == pi->a[j])); j++)
+ {
+ ;
+ }
+ }
+ else
+ {
+ for (j = 0; ((j < nral) &&
+ (get_atomtype_batype(at->atom[p->a[j]].type, atype) == pi->a[j])); j++)
+ {
+ ;
+ }
+ }
+ bFound = (j == nral);
+ }
+ if (bFound)
+ {
+ nparam_found = 1;
+ }
+ }
+
+ *param_def = pi;
+ *nparam_def = nparam_found;
+
+ return bFound;
+}
+
+
+
+void push_bond(directive d, t_params bondtype[], t_params bond[],
+ t_atoms *at, gpp_atomtype_t atype, char *line,
+ gmx_bool bBonded, gmx_bool bGenPairs, real fudgeQQ,
+ gmx_bool bZero, gmx_bool *bWarn_copy_A_B,
+ warninp_t wi)
+{
+ const char *aaformat[MAXATOMLIST] = {
+ "%d%d",
+ "%d%d%d",
+ "%d%d%d%d",
+ "%d%d%d%d%d",
+ "%d%d%d%d%d%d",
+ "%d%d%d%d%d%d%d"
+ };
+ const char *asformat[MAXATOMLIST] = {
+ "%*s%*s",
+ "%*s%*s%*s",
+ "%*s%*s%*s%*s",
+ "%*s%*s%*s%*s%*s",
+ "%*s%*s%*s%*s%*s%*s",
+ "%*s%*s%*s%*s%*s%*s%*s"
+ };
+ const char *ccformat = "%lf%lf%lf%lf%lf%lf%lf%lf%lf%lf%lf%lf%lf";
+ int nr, i, j, nral, nral_fmt, nread, ftype;
+ char format[STRLEN];
+ /* One force parameter more, so we can check if we read too many */
+ double cc[MAXFORCEPARAM+1];
+ int aa[MAXATOMLIST+1];
+ t_param param, *param_defA, *param_defB;
+ gmx_bool bFoundA = FALSE, bFoundB = FALSE, bDef, bPert, bSwapParity = FALSE;
+ int nparam_defA, nparam_defB;
+ char errbuf[256];
+
+ nparam_defA = nparam_defB = 0;
+
+ ftype = ifunc_index(d, 1);
+ nral = NRAL(ftype);
+ for (j = 0; j < MAXATOMLIST; j++)
+ {
+ aa[j] = NOTSET;
+ }
+ bDef = (NRFP(ftype) > 0);
+
+ if (ftype == F_SETTLE)
+ {
+ /* SETTLE acts on 3 atoms, but the topology format only specifies
+ * the first atom (for historical reasons).
+ */
+ nral_fmt = 1;
+ }
+ else
+ {
+ nral_fmt = nral;
+ }
+
+ nread = sscanf(line, aaformat[nral_fmt-1],
+ &aa[0], &aa[1], &aa[2], &aa[3], &aa[4], &aa[5]);
+
+ if (ftype == F_SETTLE)
+ {
+ aa[3] = aa[1];
+ aa[1] = aa[0] + 1;
+ aa[2] = aa[0] + 2;
+ }
+
+ if (nread < nral_fmt)
+ {
+ too_few(wi);
+ return;
+ }
+ else if (nread > nral_fmt)
+ {
+ /* this is a hack to allow for virtual sites with swapped parity */
+ bSwapParity = (aa[nral] < 0);
+ if (bSwapParity)
+ {
+ aa[nral] = -aa[nral];
+ }
+ ftype = ifunc_index(d, aa[nral]);
+ if (bSwapParity)
+ {
+ switch (ftype)
+ {
+ case F_VSITE3FAD:
+ case F_VSITE3OUT:
+ break;
+ default:
+ gmx_fatal(FARGS, "Negative function types only allowed for %s and %s",
+ interaction_function[F_VSITE3FAD].longname,
+ interaction_function[F_VSITE3OUT].longname);
+ }
+ }
+ }
+
+
+ /* Check for double atoms and atoms out of bounds */
+ for (i = 0; (i < nral); i++)
+ {
+ if (aa[i] < 1 || aa[i] > at->nr)
+ {
+ gmx_fatal(FARGS, "[ file %s, line %d ]:\n"
+ "Atom index (%d) in %s out of bounds (1-%d).\n"
+ "This probably means that you have inserted topology section \"%s\"\n"
+ "in a part belonging to a different molecule than you intended to.\n"
+ "In that case move the \"%s\" section to the right molecule.",
+ get_warning_file(wi), get_warning_line(wi),
+ aa[i], dir2str(d), at->nr, dir2str(d), dir2str(d));
+ }
+ for (j = i+1; (j < nral); j++)
+ {
+ if (aa[i] == aa[j])
+ {
+ sprintf(errbuf, "Duplicate atom index (%d) in %s", aa[i], dir2str(d));
+ warning(wi, errbuf);
+ }
+ }
+ }
+
+ /* default force parameters */
+ for (j = 0; (j < MAXATOMLIST); j++)
+ {
+ param.a[j] = aa[j]-1;
+ }
+ for (j = 0; (j < MAXFORCEPARAM); j++)
+ {
+ param.c[j] = 0.0;
+ }
+
+ /* Get force params for normal and free energy perturbation
+ * studies, as determined by types!
+ */
+
+ if (bBonded)
+ {
+ bFoundA = default_params(ftype, bondtype, at, atype, ¶m, FALSE, ¶m_defA, &nparam_defA);
+ if (bFoundA)
+ {
+ /* Copy the A-state and B-state default parameters. */
+ GMX_ASSERT(NRFPA(ftype)+NRFPB(ftype) <= MAXFORCEPARAM, "Bonded interactions may have at most 12 parameters");
+ for (j = 0; (j < NRFPA(ftype)+NRFPB(ftype)); j++)
+ {
+ param.c[j] = param_defA->c[j];
+ }
+ }
+ bFoundB = default_params(ftype, bondtype, at, atype, ¶m, TRUE, ¶m_defB, &nparam_defB);
+ if (bFoundB)
+ {
+ /* Copy only the B-state default parameters */
+ for (j = NRFPA(ftype); (j < NRFP(ftype)); j++)
+ {
+ param.c[j] = param_defB->c[j];
+ }
+ }
+ }
+ else if (ftype == F_LJ14)
+ {
+ bFoundA = default_nb_params(ftype, bondtype, at, ¶m, 0, FALSE, bGenPairs);
+ bFoundB = default_nb_params(ftype, bondtype, at, ¶m, 0, TRUE, bGenPairs);
+ }
+ else if (ftype == F_LJC14_Q)
+ {
+ param.c[0] = fudgeQQ;
+ /* Fill in the A-state charges as default parameters */
+ param.c[1] = at->atom[param.a[0]].q;
+ param.c[2] = at->atom[param.a[1]].q;
+ /* The default LJ parameters are the standard 1-4 parameters */
+ bFoundA = default_nb_params(F_LJ14, bondtype, at, ¶m, 3, FALSE, bGenPairs);
+ bFoundB = TRUE;
+ }
+ else if (ftype == F_LJC_PAIRS_NB)
+ {
+ /* Defaults are not supported here */
+ bFoundA = FALSE;
+ bFoundB = TRUE;
+ }
+ else
+ {
+ gmx_incons("Unknown function type in push_bond");
+ }
+
+ if (nread > nral_fmt)
+ {
+ /* Manually specified parameters - in this case we discard multiple torsion info! */
+
+ strcpy(format, asformat[nral_fmt-1]);
+ strcat(format, ccformat);
+
+ nread = sscanf(line, format, &cc[0], &cc[1], &cc[2], &cc[3], &cc[4], &cc[5],
+ &cc[6], &cc[7], &cc[8], &cc[9], &cc[10], &cc[11], &cc[12]);
+
+ if ((nread == NRFPA(ftype)) && (NRFPB(ftype) != 0))
+ {
+ /* We only have to issue a warning if these atoms are perturbed! */
+ bPert = FALSE;
+ for (j = 0; (j < nral); j++)
+ {
+ bPert = bPert || PERTURBED(at->atom[param.a[j]]);
+ }
+
+ if (bPert && *bWarn_copy_A_B)
+ {
+ sprintf(errbuf,
+ "Some parameters for bonded interaction involving perturbed atoms are specified explicitly in state A, but not B - copying A to B");
+ warning(wi, errbuf);
+ *bWarn_copy_A_B = FALSE;
+ }
+
+ /* If only the A parameters were specified, copy them to the B state */
+ /* The B-state parameters correspond to the first nrfpB
+ * A-state parameters.
+ */
+ for (j = 0; (j < NRFPB(ftype)); j++)
+ {
+ cc[nread++] = cc[j];
+ }
+ }
+
+ /* If nread was 0 or EOF, no parameters were read => use defaults.
+ * If nread was nrfpA we copied above so nread=nrfp.
+ * If nread was nrfp we are cool.
+ * For F_LJC14_Q we allow supplying fudgeQQ only.
+ * Anything else is an error!
+ */
+ if ((nread != 0) && (nread != EOF) && (nread != NRFP(ftype)) &&
+ !(ftype == F_LJC14_Q && nread == 1))
+ {
+ gmx_fatal(FARGS, "Incorrect number of parameters - found %d, expected %d or %d for %s.",
+ nread, NRFPA(ftype), NRFP(ftype),
+ interaction_function[ftype].longname);
+ }
+
+ for (j = 0; (j < nread); j++)
+ {
+ param.c[j] = cc[j];
+ }
+
+ /* Check whether we have to use the defaults */
+ if (nread == NRFP(ftype))
+ {
+ bDef = FALSE;
+ }
+ }
+ else
+ {
+ nread = 0;
+ }
+ /* nread now holds the number of force parameters read! */
+
+ if (bDef)
+ {
+ /* Use defaults */
+ /* When we have multiple terms it would be very dangerous to allow perturbations to a different atom type! */
+ if (ftype == F_PDIHS)
+ {
+ if ((nparam_defA != nparam_defB) || ((nparam_defA > 1 || nparam_defB > 1) && (param_defA != param_defB)))
+ {
+ sprintf(errbuf,
+ "Cannot automatically perturb a torsion with multiple terms to different form.\n"
+ "Please specify perturbed parameters manually for this torsion in your topology!");
+ warning_error(wi, errbuf);
+ }
+ }
+
+ if (nread > 0 && nread < NRFPA(ftype))
+ {
+ /* Issue an error, do not use defaults */
+ sprintf(errbuf, "Not enough parameters, there should be at least %d (or 0 for defaults)", NRFPA(ftype));
+ warning_error(wi, errbuf);
+ }
+
+ if (nread == 0 || nread == EOF)
+ {
+ if (!bFoundA)
+ {
+ if (interaction_function[ftype].flags & IF_VSITE)
+ {
+ /* set them to NOTSET, will be calculated later */
+ for (j = 0; (j < MAXFORCEPARAM); j++)
+ {
+ param.c[j] = NOTSET;
+ }
+
+ if (bSwapParity)
+ {
+ param.c1() = -1; /* flag to swap parity of vsite construction */
+ }
+ }
+ else
+ {
+ if (bZero)
+ {
+ fprintf(stderr, "NOTE: No default %s types, using zeroes\n",
+ interaction_function[ftype].longname);
+ }
+ else
+ {
+ sprintf(errbuf, "No default %s types", interaction_function[ftype].longname);
+ warning_error(wi, errbuf);
+ }
+ }
+ }
+ else
+ {
+ if (bSwapParity)
+ {
+ switch (ftype)
+ {
+ case F_VSITE3FAD:
+ param.c0() = 360 - param.c0();
+ break;
+ case F_VSITE3OUT:
+ param.c2() = -param.c2();
+ break;
+ }
+ }
+ }
+ if (!bFoundB)
+ {
+ /* We only have to issue a warning if these atoms are perturbed! */
+ bPert = FALSE;
+ for (j = 0; (j < nral); j++)
+ {
+ bPert = bPert || PERTURBED(at->atom[param.a[j]]);
+ }
+
+ if (bPert)
+ {
+ sprintf(errbuf, "No default %s types for perturbed atoms, "
+ "using normal values", interaction_function[ftype].longname);
+ warning(wi, errbuf);
+ }
+ }
+ }
+ }
+
+ if ((ftype == F_PDIHS || ftype == F_ANGRES || ftype == F_ANGRESZ)
+ && param.c[5] != param.c[2])
+ {
+ gmx_fatal(FARGS, "[ file %s, line %d ]:\n"
+ " %s multiplicity can not be perturbed %f!=%f",
+ get_warning_file(wi), get_warning_line(wi),
+ interaction_function[ftype].longname,
+ param.c[2], param.c[5]);
+ }
+
+ if (IS_TABULATED(ftype) && param.c[2] != param.c[0])
+ {
+ gmx_fatal(FARGS, "[ file %s, line %d ]:\n"
+ " %s table number can not be perturbed %d!=%d",
+ get_warning_file(wi), get_warning_line(wi),
+ interaction_function[ftype].longname,
+ (int)(param.c[0]+0.5), (int)(param.c[2]+0.5));
+ }
+
+ /* Dont add R-B dihedrals where all parameters are zero (no interaction) */
+ if (ftype == F_RBDIHS)
+ {
+ nr = 0;
+ for (i = 0; i < NRFP(ftype); i++)
+ {
+ if (param.c[i] != 0)
+ {
+ nr++;
+ }
+ }
+ if (nr == 0)
+ {
+ return;
+ }
+ }
+
+ /* Put the values in the appropriate arrays */
+ add_param_to_list (&bond[ftype], ¶m);
+
+ /* Push additional torsions from FF for ftype==9 if we have them.
+ * We have already checked that the A/B states do not differ in this case,
+ * so we do not have to double-check that again, or the vsite stuff.
+ * In addition, those torsions cannot be automatically perturbed.
+ */
+ if (bDef && ftype == F_PDIHS)
+ {
+ for (i = 1; i < nparam_defA; i++)
+ {
+ /* Advance pointer! */
+ param_defA += 2;
+ for (j = 0; (j < NRFPA(ftype)+NRFPB(ftype)); j++)
+ {
+ param.c[j] = param_defA->c[j];
+ }
+ /* And push the next term for this torsion */
+ add_param_to_list (&bond[ftype], ¶m);
+ }
+ }
+}
+
+void push_cmap(directive d, t_params bondtype[], t_params bond[],
+ t_atoms *at, gpp_atomtype_t atype, char *line,
+ warninp_t wi)
+{
+ const char *aaformat[MAXATOMLIST+1] =
+ {
+ "%d",
+ "%d%d",
+ "%d%d%d",
+ "%d%d%d%d",
+ "%d%d%d%d%d",
+ "%d%d%d%d%d%d",
+ "%d%d%d%d%d%d%d"
+ };
+
+ int i, j, ftype, nral, nread, ncmap_params;
+ int cmap_type;
+ int aa[MAXATOMLIST+1];
+ char errbuf[256];
+ gmx_bool bFound;
+ t_param param;
+
+ ftype = ifunc_index(d, 1);
+ nral = NRAL(ftype);
+ ncmap_params = 0;
+
+ nread = sscanf(line, aaformat[nral-1],
+ &aa[0], &aa[1], &aa[2], &aa[3], &aa[4], &aa[5]);
+
+ if (nread < nral)
+ {
+ too_few(wi);
+ return;
+ }
+ else if (nread == nral)
+ {
+ ftype = ifunc_index(d, 1);
+ }
+
+ /* Check for double atoms and atoms out of bounds */
+ for (i = 0; i < nral; i++)
+ {
+ if (aa[i] < 1 || aa[i] > at->nr)
+ {
+ gmx_fatal(FARGS, "[ file %s, line %d ]:\n"
+ "Atom index (%d) in %s out of bounds (1-%d).\n"
+ "This probably means that you have inserted topology section \"%s\"\n"
+ "in a part belonging to a different molecule than you intended to.\n"
+ "In that case move the \"%s\" section to the right molecule.",
+ get_warning_file(wi), get_warning_line(wi),
+ aa[i], dir2str(d), at->nr, dir2str(d), dir2str(d));
+ }
+
+ for (j = i+1; (j < nral); j++)
+ {
+ if (aa[i] == aa[j])
+ {
+ sprintf(errbuf, "Duplicate atom index (%d) in %s", aa[i], dir2str(d));
+ warning(wi, errbuf);
+ }
+ }
+ }
+
+ /* default force parameters */
+ for (j = 0; (j < MAXATOMLIST); j++)
+ {
+ param.a[j] = aa[j]-1;
+ }
+ for (j = 0; (j < MAXFORCEPARAM); j++)
+ {
+ param.c[j] = 0.0;
+ }
+
+ /* Get the cmap type for this cmap angle */
+ bFound = default_cmap_params(bondtype, at, atype, ¶m, FALSE, &cmap_type, &ncmap_params);
+
+ /* We want exactly one parameter (the cmap type in state A (currently no state B) back */
+ if (bFound && ncmap_params == 1)
+ {
+ /* Put the values in the appropriate arrays */
+ param.c[0] = cmap_type;
+ add_param_to_list(&bond[ftype], ¶m);
+ }
+ else
+ {
+ /* This is essentially the same check as in default_cmap_params() done one more time */
+ gmx_fatal(FARGS, "Unable to assign a cmap type to torsion %d %d %d %d and %d\n",
+ param.a[0]+1, param.a[1]+1, param.a[2]+1, param.a[3]+1, param.a[4]+1);
+ }
+}
+
+
+
+void push_vsitesn(directive d, t_params bond[],
+ t_atoms *at, char *line,
+ warninp_t wi)
+{
+ char *ptr;
+ int type, ftype, j, n, ret, nj, a;
+ int *atc = NULL;
+ double *weight = NULL, weight_tot;
+ t_param param;
+
+ /* default force parameters */
+ for (j = 0; (j < MAXATOMLIST); j++)
+ {
+ param.a[j] = NOTSET;
+ }
+ for (j = 0; (j < MAXFORCEPARAM); j++)
+ {
+ param.c[j] = 0.0;
+ }
+
+ ptr = line;
+ ret = sscanf(ptr, "%d%n", &a, &n);
+ ptr += n;
+ if (ret == 0)
+ {
+ gmx_fatal(FARGS, "[ file %s, line %d ]:\n"
+ " Expected an atom index in section \"%s\"",
+ get_warning_file(wi), get_warning_line(wi),
+ dir2str(d));
+ }
+
+ param.a[0] = a - 1;
+
+ sscanf(ptr, "%d%n", &type, &n);
+ ptr += n;
+ ftype = ifunc_index(d, type);
+
+ weight_tot = 0;
+ nj = 0;
+ do
+ {
+ ret = sscanf(ptr, "%d%n", &a, &n);
+ ptr += n;
+ if (ret > 0)
+ {
+ if (nj % 20 == 0)
+ {
+ srenew(atc, nj+20);
+ srenew(weight, nj+20);
+ }
+ atc[nj] = a - 1;
+ switch (type)
+ {
+ case 1:
+ weight[nj] = 1;
+ break;
+ case 2:
+ /* Here we use the A-state mass as a parameter.
+ * Note that the B-state mass has no influence.
+ */
+ weight[nj] = at->atom[atc[nj]].m;
+ break;
+ case 3:
+ weight[nj] = -1;
+ ret = sscanf(ptr, "%lf%n", &(weight[nj]), &n);
+ ptr += n;
+ if (weight[nj] < 0)
+ {
+ gmx_fatal(FARGS, "[ file %s, line %d ]:\n"
+ " No weight or negative weight found for vsiten constructing atom %d (atom index %d)",
+ get_warning_file(wi), get_warning_line(wi),
+ nj+1, atc[nj]+1);
+ }
+ break;
+ default:
+ gmx_fatal(FARGS, "Unknown vsiten type %d", type);
+ }
+ weight_tot += weight[nj];
+ nj++;
+ }
+ }
+ while (ret > 0);
+
+ if (nj == 0)
+ {
+ gmx_fatal(FARGS, "[ file %s, line %d ]:\n"
+ " Expected more than one atom index in section \"%s\"",
+ get_warning_file(wi), get_warning_line(wi),
+ dir2str(d));
+ }
+
+ if (weight_tot == 0)
+ {
+ gmx_fatal(FARGS, "[ file %s, line %d ]:\n"
+ " The total mass of the construting atoms is zero",
+ get_warning_file(wi), get_warning_line(wi));
+ }
+
+ for (j = 0; j < nj; j++)
+ {
+ param.a[1] = atc[j];
+ param.c[0] = nj;
+ param.c[1] = weight[j]/weight_tot;
+ /* Put the values in the appropriate arrays */
+ add_param_to_list (&bond[ftype], ¶m);
+ }
+
+ sfree(atc);
+ sfree(weight);
+}
+
+void push_mol(int nrmols, t_molinfo mols[], char *pline, int *whichmol,
+ int *nrcopies,
+ warninp_t wi)
+{
+ char type[STRLEN];
+
+ if (sscanf(pline, "%s%d", type, nrcopies) != 2)
+ {
+ too_few(wi);
+ return;
+ }
+
+ /* Search moleculename.
+ * Here we originally only did case insensitive matching. But because
+ * some PDB files can have many chains and use case to generate more
+ * chain-identifiers, which in turn end up in our moleculetype name,
+ * we added support for case-sensitivity.
+ */
+ int nrcs = 0;
+ int nrci = 0;
+ int matchci = -1;
+ int matchcs = -1;
+ for (int i = 0; i < nrmols; i++)
+ {
+ if (strcmp(type, *(mols[i].name)) == 0)
+ {
+ nrcs++;
+ matchcs = i;
+ }
+ if (gmx_strcasecmp(type, *(mols[i].name)) == 0)
+ {
+ nrci++;
+ matchci = i;
+ }
+ }
+
+ if (nrcs == 1)
+ {
+ // select the case sensitive match
+ *whichmol = matchcs;
+ }
+ else
+ {
+ // avoid matching case-insensitive when we have multiple matches
+ if (nrci > 1)
+ {
+ gmx_fatal(FARGS, "For moleculetype '%s' in [ system ] %d case insensitive matches, but %d case sensitive matches were found. Check the case of the characters in the moleculetypes.", type, nrci, nrcs);
+ }
+ if (nrci == 1)
+ {
+ // select the unique case insensitive match
+ *whichmol = matchci;
+ }
+ else
+ {
+ gmx_fatal(FARGS, "No such moleculetype %s", type);
+ }
+ }
+}
+
+void init_block2(t_block2 *b2, int natom)
+{
+ int i;
+
+ b2->nr = natom;
+ snew(b2->nra, b2->nr);
+ snew(b2->a, b2->nr);
+ for (i = 0; (i < b2->nr); i++)
+ {
+ b2->a[i] = NULL;
+ }
+}
+
+void done_block2(t_block2 *b2)
+{
+ int i;
+
+ if (b2->nr)
+ {
+ for (i = 0; (i < b2->nr); i++)
+ {
+ sfree(b2->a[i]);
+ }
+ sfree(b2->a);
+ sfree(b2->nra);
+ b2->nr = 0;
+ }
+}
+
+void push_excl(char *line, t_block2 *b2)
+{
+ int i, j;
+ int n;
+ char base[STRLEN], format[STRLEN];
+
+ if (sscanf(line, "%d", &i) == 0)
+ {
+ return;
+ }
+
+ if ((1 <= i) && (i <= b2->nr))
+ {
+ i--;
+ }
+ else
+ {
+ if (debug)
+ {
+ fprintf(debug, "Unbound atom %d\n", i-1);
+ }
+ return;
+ }
+ strcpy(base, "%*d");
+ do
+ {
+ strcpy(format, base);
+ strcat(format, "%d");
+ n = sscanf(line, format, &j);
+ if (n == 1)
+ {
+ if ((1 <= j) && (j <= b2->nr))
+ {
+ j--;
+ srenew(b2->a[i], ++(b2->nra[i]));
+ b2->a[i][b2->nra[i]-1] = j;
+ /* also add the reverse exclusion! */
+ srenew(b2->a[j], ++(b2->nra[j]));
+ b2->a[j][b2->nra[j]-1] = i;
+ strcat(base, "%*d");
+ }
+ else
+ {
+ gmx_fatal(FARGS, "Invalid Atomnr j: %d, b2->nr: %d\n", j, b2->nr);
+ }
+ }
+ }
+ while (n == 1);
+}
+
+void b_to_b2(t_blocka *b, t_block2 *b2)
+{
+ int i;
+ int j, a;
+
+ for (i = 0; (i < b->nr); i++)
+ {
+ for (j = b->index[i]; (j < b->index[i+1]); j++)
+ {
+ a = b->a[j];
+ srenew(b2->a[i], ++b2->nra[i]);
+ b2->a[i][b2->nra[i]-1] = a;
+ }
+ }
+}
+
+void b2_to_b(t_block2 *b2, t_blocka *b)
+{
+ int i, nra;
+ int j;
+
+ nra = 0;
+ for (i = 0; (i < b2->nr); i++)
+ {
+ b->index[i] = nra;
+ for (j = 0; (j < b2->nra[i]); j++)
+ {
+ b->a[nra+j] = b2->a[i][j];
+ }
+ nra += b2->nra[i];
+ }
+ /* terminate list */
+ b->index[i] = nra;
+}
+
+static int icomp(const void *v1, const void *v2)
+{
+ return (*((int *) v1))-(*((int *) v2));
+}
+
+void merge_excl(t_blocka *excl, t_block2 *b2)
+{
+ int i, k;
+ int j;
+ int nra;
+
+ if (!b2->nr)
+ {
+ return;
+ }
+ else if (b2->nr != excl->nr)
+ {
+ gmx_fatal(FARGS, "DEATH HORROR: b2->nr = %d, while excl->nr = %d",
+ b2->nr, excl->nr);
+ }
+ else if (debug)
+ {
+ fprintf(debug, "Entering merge_excl\n");
+ }
+
+ /* First copy all entries from excl to b2 */
+ b_to_b2(excl, b2);
+
+ /* Count and sort the exclusions */
+ nra = 0;
+ for (i = 0; (i < b2->nr); i++)
+ {
+ if (b2->nra[i] > 0)
+ {
+ /* remove double entries */
+ qsort(b2->a[i], (size_t)b2->nra[i], (size_t)sizeof(b2->a[i][0]), icomp);
+ k = 1;
+ for (j = 1; (j < b2->nra[i]); j++)
+ {
+ if (b2->a[i][j] != b2->a[i][k-1])
+ {
+ b2->a[i][k] = b2->a[i][j];
+ k++;
+ }
+ }
+ b2->nra[i] = k;
+ nra += b2->nra[i];
+ }
+ }
+ excl->nra = nra;
+ srenew(excl->a, excl->nra);
+
+ b2_to_b(b2, excl);
+}
+
+int add_atomtype_decoupled(t_symtab *symtab, gpp_atomtype_t at,
+ t_nbparam ***nbparam, t_nbparam ***pair)
+{
+ t_atom atom;
+ t_param param;
+ int i, nr;
+
+ /* Define an atom type with all parameters set to zero (no interactions) */
+ atom.q = 0.0;
+ atom.m = 0.0;
+ /* Type for decoupled atoms could be anything,
+ * this should be changed automatically later when required.
+ */
+ atom.ptype = eptAtom;
+ for (i = 0; (i < MAXFORCEPARAM); i++)
+ {
+ param.c[i] = 0.0;
+ }
+
+ nr = add_atomtype(at, symtab, &atom, "decoupled", ¶m, -1, 0.0, 0.0, 0.0, 0, 0, 0);
+
+ /* Add space in the non-bonded parameters matrix */
+ realloc_nb_params(at, nbparam, pair);
+
+ return nr;
+}
+
+static void convert_pairs_to_pairsQ(t_params *plist,
+ real fudgeQQ, t_atoms *atoms)
+{
+ t_param *paramp1, *paramp2, *paramnew;
+ int i, j, p1nr, p2nr, p2newnr;
+
+ /* Add the pair list to the pairQ list */
+ p1nr = plist[F_LJ14].nr;
+ p2nr = plist[F_LJC14_Q].nr;
+ p2newnr = p1nr + p2nr;
+ snew(paramnew, p2newnr);
+
+ paramp1 = plist[F_LJ14].param;
+ paramp2 = plist[F_LJC14_Q].param;
+
+ /* Fill in the new F_LJC14_Q array with the old one. NOTE:
+ it may be possible to just ADD the converted F_LJ14 array
+ to the old F_LJC14_Q array, but since we have to create
+ a new sized memory structure, better just to deep copy it all.
+ */
+
+ for (i = 0; i < p2nr; i++)
+ {
+ /* Copy over parameters */
+ for (j = 0; j < 5; j++) /* entries are 0-4 for F_LJC14_Q */
+ {
+ paramnew[i].c[j] = paramp2[i].c[j];
+ }
+
+ /* copy over atoms */
+ for (j = 0; j < 2; j++)
+ {
+ paramnew[i].a[j] = paramp2[i].a[j];
+ }
+ }
+
+ for (i = p2nr; i < p2newnr; i++)
+ {
+ j = i-p2nr;
+
+ /* Copy over parameters */
+ paramnew[i].c[0] = fudgeQQ;
+ paramnew[i].c[1] = atoms->atom[paramp1[j].a[0]].q;
+ paramnew[i].c[2] = atoms->atom[paramp1[j].a[1]].q;
+ paramnew[i].c[3] = paramp1[j].c[0];
+ paramnew[i].c[4] = paramp1[j].c[1];
+
+ /* copy over atoms */
+ paramnew[i].a[0] = paramp1[j].a[0];
+ paramnew[i].a[1] = paramp1[j].a[1];
+ }
+
+ /* free the old pairlists */
+ sfree(plist[F_LJC14_Q].param);
+ sfree(plist[F_LJ14].param);
+
+ /* now assign the new data to the F_LJC14_Q structure */
+ plist[F_LJC14_Q].param = paramnew;
+ plist[F_LJC14_Q].nr = p2newnr;
+
+ /* Empty the LJ14 pairlist */
+ plist[F_LJ14].nr = 0;
+ plist[F_LJ14].param = NULL;
+}
+
+static void generate_LJCpairsNB(t_molinfo *mol, int nb_funct, t_params *nbp)
+{
+ int n, ntype, i, j, k;
+ t_atom *atom;
+ t_blocka *excl;
+ gmx_bool bExcl;
+ t_param param;
+
+ n = mol->atoms.nr;
+ atom = mol->atoms.atom;
+
+ ntype = static_cast<int>(std::sqrt(static_cast<double>(nbp->nr)));
+ GMX_ASSERT(ntype * ntype == nbp->nr, "Number of pairs of generated non-bonded parameters should be a perfect square");
+
+ for (i = 0; i < MAXATOMLIST; i++)
+ {
+ param.a[i] = NOTSET;
+ }
+ for (i = 0; i < MAXFORCEPARAM; i++)
+ {
+ param.c[i] = NOTSET;
+ }
+
+ /* Add a pair interaction for all non-excluded atom pairs */
+ excl = &mol->excls;
+ for (i = 0; i < n; i++)
+ {
+ for (j = i+1; j < n; j++)
+ {
+ bExcl = FALSE;
+ for (k = excl->index[i]; k < excl->index[i+1]; k++)
+ {
+ if (excl->a[k] == j)
+ {
+ bExcl = TRUE;
+ }
+ }
+ if (!bExcl)
+ {
+ if (nb_funct != F_LJ)
+ {
+ gmx_fatal(FARGS, "Can only generate non-bonded pair interactions for Van der Waals type Lennard-Jones");
+ }
+ param.a[0] = i;
+ param.a[1] = j;
+ param.c[0] = atom[i].q;
+ param.c[1] = atom[j].q;
+ param.c[2] = nbp->param[ntype*atom[i].type+atom[j].type].c[0];
+ param.c[3] = nbp->param[ntype*atom[i].type+atom[j].type].c[1];
+ add_param_to_list(&mol->plist[F_LJC_PAIRS_NB], ¶m);
+ }
+ }
+ }
+}
+
+static void set_excl_all(t_blocka *excl)
+{
+ int nat, i, j, k;
+
+ /* Get rid of the current exclusions and exclude all atom pairs */
+ nat = excl->nr;
+ excl->nra = nat*nat;
+ srenew(excl->a, excl->nra);
+ k = 0;
+ for (i = 0; i < nat; i++)
+ {
+ excl->index[i] = k;
+ for (j = 0; j < nat; j++)
+ {
+ excl->a[k++] = j;
+ }
+ }
+ excl->index[nat] = k;
+}
+
+static void decouple_atoms(t_atoms *atoms, int atomtype_decouple,
- atoms->atom[i].q = 0.0;
++ int couple_lam0, int couple_lam1,
++ const char *mol_name)
+{
+ int i;
+
+ for (i = 0; i < atoms->nr; i++)
+ {
++ t_atom *atom;
++
++ atom = &atoms->atom[i];
++
++ if (atom->qB != atom->q || atom->typeB != atom->type)
++ {
++ gmx_fatal(FARGS, "Atom %d in molecule type '%s' has different A and B state charges and/or atom types set in the topology file as well as through the mdp option '%s'. You can not use both these methods simultaneously.",
++ i + 1, mol_name, "couple-moltype");
++ }
++
+ if (couple_lam0 == ecouplamNONE || couple_lam0 == ecouplamVDW)
+ {
- atoms->atom[i].type = atomtype_decouple;
++ atom->q = 0.0;
+ }
+ if (couple_lam0 == ecouplamNONE || couple_lam0 == ecouplamQ)
+ {
- atoms->atom[i].qB = 0.0;
++ atom->type = atomtype_decouple;
+ }
+ if (couple_lam1 == ecouplamNONE || couple_lam1 == ecouplamVDW)
+ {
- atoms->atom[i].typeB = atomtype_decouple;
++ atom->qB = 0.0;
+ }
+ if (couple_lam1 == ecouplamNONE || couple_lam1 == ecouplamQ)
+ {
- decouple_atoms(&mol->atoms, atomtype_decouple, couple_lam0, couple_lam1);
++ atom->typeB = atomtype_decouple;
+ }
+ }
+}
+
+void convert_moltype_couple(t_molinfo *mol, int atomtype_decouple, real fudgeQQ,
+ int couple_lam0, int couple_lam1,
+ gmx_bool bCoupleIntra, int nb_funct, t_params *nbp)
+{
+ convert_pairs_to_pairsQ(mol->plist, fudgeQQ, &mol->atoms);
+ if (!bCoupleIntra)
+ {
+ generate_LJCpairsNB(mol, nb_funct, nbp);
+ set_excl_all(&mol->excls);
+ }
++ decouple_atoms(&mol->atoms, atomtype_decouple, couple_lam0, couple_lam1,
++ *mol->name);
+}
--- /dev/null
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
++ * Copyright (c) 2012,2013,2014,2015,2016, 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 "gmxpre.h"
+
+#include "calc_verletbuf.h"
+
+#include <assert.h>
+#include <stdlib.h>
+
+#include <cmath>
+
+#include <algorithm>
+
+#include "gromacs/math/calculate-ewald-splitting-coefficient.h"
+#include "gromacs/math/functions.h"
+#include "gromacs/math/units.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/mdlib/nb_verlet.h"
+#include "gromacs/mdlib/nbnxn_simd.h"
+#include "gromacs/mdlib/nbnxn_util.h"
+#include "gromacs/mdtypes/inputrec.h"
+#include "gromacs/mdtypes/md_enums.h"
+#include "gromacs/topology/ifunc.h"
+#include "gromacs/topology/topology.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/smalloc.h"
+
+/* The code in this file estimates a pairlist buffer length
+ * given a target energy drift per atom per picosecond.
+ * This is done by estimating the drift given a buffer length.
+ * Ideally we would like to have a tight overestimate of the drift,
+ * but that can be difficult to achieve.
+ *
+ * Significant approximations used:
+ *
+ * Uniform particle density. UNDERESTIMATES the drift by rho_global/rho_local.
+ *
+ * Interactions don't affect particle motion. OVERESTIMATES the drift on longer
+ * time scales. This approximation probably introduces the largest errors.
+ *
+ * Only take one constraint per particle into account: OVERESTIMATES the drift.
+ *
+ * For rotating constraints assume the same functional shape for time scales
+ * where the constraints rotate significantly as the exact expression for
+ * short time scales. OVERESTIMATES the drift on long time scales.
+ *
+ * For non-linear virtual sites use the mass of the lightest constructing atom
+ * to determine the displacement. OVER/UNDERESTIMATES the drift, depending on
+ * the geometry and masses of constructing atoms.
+ *
+ * Note that the formulas for normal atoms and linear virtual sites are exact,
+ * apart from the first two approximations.
+ *
+ * Note that apart from the effect of the above approximations, the actual
+ * drift of the total energy of a system can be order of magnitude smaller
+ * due to cancellation of positive and negative drift for different pairs.
+ */
+
+
+/* Struct for unique atom type for calculating the energy drift.
+ * The atom displacement depends on mass and constraints.
+ * The energy jump for given distance depend on LJ type and q.
+ */
+typedef struct
+{
+ real mass; /* mass */
+ int type; /* type (used for LJ parameters) */
+ real q; /* charge */
+ gmx_bool bConstr; /* constrained, if TRUE, use #DOF=2 iso 3 */
+ real con_mass; /* mass of heaviest atom connected by constraints */
+ real con_len; /* constraint length to the heaviest atom */
+} atom_nonbonded_kinetic_prop_t;
+
+/* Struct for unique atom type for calculating the energy drift.
+ * The atom displacement depends on mass and constraints.
+ * The energy jump for given distance depend on LJ type and q.
+ */
+typedef struct
+{
+ atom_nonbonded_kinetic_prop_t prop; /* non-bonded and kinetic atom prop. */
+ int n; /* #atoms of this type in the system */
+} verletbuf_atomtype_t;
+
+void verletbuf_get_list_setup(gmx_bool gmx_unused bSIMD,
+ gmx_bool bGPU,
+ verletbuf_list_setup_t *list_setup)
+{
+ /* When calling this function we often don't know which kernel type we
+ * are going to use. W choose the kernel type with the smallest possible
+ * i- and j-cluster sizes, so we potentially overestimate, but never
+ * underestimate, the buffer drift.
+ * Note that the current buffer estimation code only handles clusters
+ * of size 1, 2 or 4, so for 4x8 or 8x8 we use the estimate for 4x4.
+ */
+
+ if (bGPU)
+ {
+ /* The CUDA kernels split the j-clusters in two halves */
+ list_setup->cluster_size_i = nbnxn_kernel_to_cluster_i_size(nbnxnk8x8x8_GPU);
+ list_setup->cluster_size_j = nbnxn_kernel_to_cluster_j_size(nbnxnk8x8x8_GPU)/2;
+ }
+ else
+ {
+ int kernel_type;
+
+ kernel_type = nbnxnk4x4_PlainC;
+
+#if GMX_SIMD
+ if (bSIMD)
+ {
+#ifdef GMX_NBNXN_SIMD_2XNN
+ /* We use the smallest cluster size to be on the safe side */
+ kernel_type = nbnxnk4xN_SIMD_2xNN;
+#else
+ kernel_type = nbnxnk4xN_SIMD_4xN;
+#endif
+ }
+#endif
+
+ list_setup->cluster_size_i = nbnxn_kernel_to_cluster_i_size(kernel_type);
+ list_setup->cluster_size_j = nbnxn_kernel_to_cluster_j_size(kernel_type);
+ }
+}
+
+static gmx_bool
+atom_nonbonded_kinetic_prop_equal(const atom_nonbonded_kinetic_prop_t *prop1,
+ const atom_nonbonded_kinetic_prop_t *prop2)
+{
+ return (prop1->mass == prop2->mass &&
+ prop1->type == prop2->type &&
+ prop1->q == prop2->q &&
+ prop1->bConstr == prop2->bConstr &&
+ prop1->con_mass == prop2->con_mass &&
+ prop1->con_len == prop2->con_len);
+}
+
+static void add_at(verletbuf_atomtype_t **att_p, int *natt_p,
+ const atom_nonbonded_kinetic_prop_t *prop,
+ int nmol)
+{
+ verletbuf_atomtype_t *att;
+ int natt, i;
+
+ if (prop->mass == 0)
+ {
+ /* Ignore massless particles */
+ return;
+ }
+
+ att = *att_p;
+ natt = *natt_p;
+
+ i = 0;
+ while (i < natt && !atom_nonbonded_kinetic_prop_equal(prop, &att[i].prop))
+ {
+ i++;
+ }
+
+ if (i < natt)
+ {
+ att[i].n += nmol;
+ }
+ else
+ {
+ (*natt_p)++;
+ srenew(*att_p, *natt_p);
+ (*att_p)[i].prop = *prop;
+ (*att_p)[i].n = nmol;
+ }
+}
+
+static void get_vsite_masses(const gmx_moltype_t *moltype,
+ const gmx_ffparams_t *ffparams,
+ real *vsite_m,
+ int *n_nonlin_vsite)
+{
+ int ft, i;
+ const t_ilist *il;
+
+ *n_nonlin_vsite = 0;
+
+ /* Check for virtual sites, determine mass from constructing atoms */
+ for (ft = 0; ft < F_NRE; ft++)
+ {
+ if (IS_VSITE(ft))
+ {
+ il = &moltype->ilist[ft];
+
+ for (i = 0; i < il->nr; i += 1+NRAL(ft))
+ {
+ const t_iparams *ip;
+ real inv_mass, coeff, m_aj;
+ int a1, aj;
+
+ ip = &ffparams->iparams[il->iatoms[i]];
+
+ a1 = il->iatoms[i+1];
+
+ if (ft != F_VSITEN)
+ {
+ /* Only vsiten can have more than four
+ constructing atoms, so NRAL(ft) <= 5 */
+ int j;
+ real *cam;
+ const int maxj = NRAL(ft);
+
+ snew(cam, maxj);
+ assert(maxj <= 5);
+ for (j = 1; j < maxj; j++)
+ {
+ cam[j] = moltype->atoms.atom[il->iatoms[i+1+j]].m;
+ if (cam[j] == 0)
+ {
+ cam[j] = vsite_m[il->iatoms[i+1+j]];
+ }
+ if (cam[j] == 0)
+ {
+ gmx_fatal(FARGS, "In molecule type '%s' %s construction involves atom %d, which is a virtual site of equal or high complexity. This is not supported.",
+ *moltype->name,
+ interaction_function[ft].longname,
+ il->iatoms[i+1+j]+1);
+ }
+ }
+
+ switch (ft)
+ {
+ case F_VSITE2:
+ /* Exact */
+ vsite_m[a1] = (cam[1]*cam[2])/(cam[2]*gmx::square(1-ip->vsite.a) + cam[1]*gmx::square(ip->vsite.a));
+ break;
+ case F_VSITE3:
+ /* Exact */
+ vsite_m[a1] = (cam[1]*cam[2]*cam[3])/(cam[2]*cam[3]*gmx::square(1-ip->vsite.a-ip->vsite.b) + cam[1]*cam[3]*gmx::square(ip->vsite.a) + cam[1]*cam[2]*gmx::square(ip->vsite.b));
+ break;
+ case F_VSITEN:
+ gmx_incons("Invalid vsite type");
+ break;
+ default:
+ /* Use the mass of the lightest constructing atom.
+ * This is an approximation.
+ * If the distance of the virtual site to the
+ * constructing atom is less than all distances
+ * between constructing atoms, this is a safe
+ * over-estimate of the displacement of the vsite.
+ * This condition holds for all H mass replacement
+ * vsite constructions, except for SP2/3 groups.
+ * In SP3 groups one H will have a F_VSITE3
+ * construction, so even there the total drift
+ * estimate shouldn't be far off.
+ */
+ vsite_m[a1] = cam[1];
+ for (j = 2; j < maxj; j++)
+ {
+ vsite_m[a1] = std::min(vsite_m[a1], cam[j]);
+ }
+ (*n_nonlin_vsite)++;
+ break;
+ }
+ sfree(cam);
+ }
+ else
+ {
+ int j;
+
+ /* Exact */
+ inv_mass = 0;
+ for (j = 0; j < 3*ffparams->iparams[il->iatoms[i]].vsiten.n; j += 3)
+ {
+ aj = il->iatoms[i+j+2];
+ coeff = ffparams->iparams[il->iatoms[i+j]].vsiten.a;
+ if (moltype->atoms.atom[aj].ptype == eptVSite)
+ {
+ m_aj = vsite_m[aj];
+ }
+ else
+ {
+ m_aj = moltype->atoms.atom[aj].m;
+ }
+ if (m_aj <= 0)
+ {
+ gmx_incons("The mass of a vsiten constructing atom is <= 0");
+ }
+ inv_mass += coeff*coeff/m_aj;
+ }
+ vsite_m[a1] = 1/inv_mass;
+ /* Correct for loop increment of i */
+ i += j - 1 - NRAL(ft);
+ }
+ if (gmx_debug_at)
+ {
+ fprintf(debug, "atom %4d %-20s mass %6.3f\n",
+ a1, interaction_function[ft].longname, vsite_m[a1]);
+ }
+ }
+ }
+ }
+}
+
+static void get_verlet_buffer_atomtypes(const gmx_mtop_t *mtop,
+ verletbuf_atomtype_t **att_p,
+ int *natt_p,
+ int *n_nonlin_vsite)
+{
+ verletbuf_atomtype_t *att;
+ int natt;
+ int mb, nmol, ft, i, a1, a2, a3, a;
+ const t_atoms *atoms;
+ const t_ilist *il;
+ const t_iparams *ip;
+ atom_nonbonded_kinetic_prop_t *prop;
+ real *vsite_m;
+ int n_nonlin_vsite_mol;
+
+ att = NULL;
+ natt = 0;
+
+ if (n_nonlin_vsite != NULL)
+ {
+ *n_nonlin_vsite = 0;
+ }
+
+ for (mb = 0; mb < mtop->nmolblock; mb++)
+ {
+ nmol = mtop->molblock[mb].nmol;
+
+ atoms = &mtop->moltype[mtop->molblock[mb].type].atoms;
+
+ /* Check for constraints, as they affect the kinetic energy.
+ * For virtual sites we need the masses and geometry of
+ * the constructing atoms to determine their velocity distribution.
+ */
+ snew(prop, atoms->nr);
+ snew(vsite_m, atoms->nr);
+
+ for (ft = F_CONSTR; ft <= F_CONSTRNC; ft++)
+ {
+ il = &mtop->moltype[mtop->molblock[mb].type].ilist[ft];
+
+ for (i = 0; i < il->nr; i += 1+NRAL(ft))
+ {
+ ip = &mtop->ffparams.iparams[il->iatoms[i]];
+ a1 = il->iatoms[i+1];
+ a2 = il->iatoms[i+2];
+ if (atoms->atom[a2].m > prop[a1].con_mass)
+ {
+ prop[a1].con_mass = atoms->atom[a2].m;
+ prop[a1].con_len = ip->constr.dA;
+ }
+ if (atoms->atom[a1].m > prop[a2].con_mass)
+ {
+ prop[a2].con_mass = atoms->atom[a1].m;
+ prop[a2].con_len = ip->constr.dA;
+ }
+ }
+ }
+
+ il = &mtop->moltype[mtop->molblock[mb].type].ilist[F_SETTLE];
+
+ for (i = 0; i < il->nr; i += 1+NRAL(F_SETTLE))
+ {
+ ip = &mtop->ffparams.iparams[il->iatoms[i]];
+ a1 = il->iatoms[i+1];
+ a2 = il->iatoms[i+2];
+ a3 = il->iatoms[i+3];
+ /* Usually the mass of a1 (usually oxygen) is larger than a2/a3.
+ * If this is not the case, we overestimate the displacement,
+ * which leads to a larger buffer (ok since this is an exotic case).
+ */
+ prop[a1].con_mass = atoms->atom[a2].m;
+ prop[a1].con_len = ip->settle.doh;
+
+ prop[a2].con_mass = atoms->atom[a1].m;
+ prop[a2].con_len = ip->settle.doh;
+
+ prop[a3].con_mass = atoms->atom[a1].m;
+ prop[a3].con_len = ip->settle.doh;
+ }
+
+ get_vsite_masses(&mtop->moltype[mtop->molblock[mb].type],
+ &mtop->ffparams,
+ vsite_m,
+ &n_nonlin_vsite_mol);
+ if (n_nonlin_vsite != NULL)
+ {
+ *n_nonlin_vsite += nmol*n_nonlin_vsite_mol;
+ }
+
+ for (a = 0; a < atoms->nr; a++)
+ {
+ if (atoms->atom[a].ptype == eptVSite)
+ {
+ prop[a].mass = vsite_m[a];
+ }
+ else
+ {
+ prop[a].mass = atoms->atom[a].m;
+ }
+ prop[a].type = atoms->atom[a].type;
+ prop[a].q = atoms->atom[a].q;
+ /* We consider an atom constrained, #DOF=2, when it is
+ * connected with constraints to (at least one) atom with
+ * a mass of more than 0.4x its own mass. This is not a critical
+ * parameter, since with roughly equal masses the unconstrained
+ * and constrained displacement will not differ much (and both
+ * overestimate the displacement).
+ */
+ prop[a].bConstr = (prop[a].con_mass > 0.4*prop[a].mass);
+
+ add_at(&att, &natt, &prop[a], nmol);
+ }
+
+ sfree(vsite_m);
+ sfree(prop);
+ }
+
+ if (gmx_debug_at)
+ {
+ for (a = 0; a < natt; a++)
+ {
+ fprintf(debug, "type %d: m %5.2f t %d q %6.3f con %d con_m %5.3f con_l %5.3f n %d\n",
+ a, att[a].prop.mass, att[a].prop.type, att[a].prop.q,
+ att[a].prop.bConstr, att[a].prop.con_mass, att[a].prop.con_len,
+ att[a].n);
+ }
+ }
+
+ *att_p = att;
+ *natt_p = natt;
+}
+
+/* This function computes two components of the estimate of the variance
+ * in the displacement of one atom in a system of two constrained atoms.
+ * Returns in sigma2_2d the variance due to rotation of the constrained
+ * atom around the atom to which it constrained.
+ * Returns in sigma2_3d the variance due to displacement of the COM
+ * of the whole system of the two constrained atoms.
+ *
+ * Note that we only take a single constraint (the one to the heaviest atom)
+ * into account. If an atom has multiple constraints, this will result in
+ * an overestimate of the displacement, which gives a larger drift and buffer.
+ */
+static void constrained_atom_sigma2(real kT_fac,
+ const atom_nonbonded_kinetic_prop_t *prop,
+ real *sigma2_2d,
+ real *sigma2_3d)
+{
+ real sigma2_rot;
+ real com_dist;
+ real sigma2_rel;
+ real scale;
+
+ /* Here we decompose the motion of a constrained atom into two
+ * components: rotation around the COM and translation of the COM.
+ */
+
+ /* Determine the variance for the displacement of the rotational mode */
+ sigma2_rot = kT_fac/(prop->mass*(prop->mass + prop->con_mass)/prop->con_mass);
+
+ /* The distance from the atom to the COM, i.e. the rotational arm */
+ com_dist = prop->con_len*prop->con_mass/(prop->mass + prop->con_mass);
+
+ /* The variance relative to the arm */
+ sigma2_rel = sigma2_rot/(com_dist*com_dist);
+ /* At 6 the scaling formula has slope 0,
+ * so we keep sigma2_2d constant after that.
+ */
+ if (sigma2_rel < 6)
+ {
+ /* A constrained atom rotates around the atom it is constrained to.
+ * This results in a smaller linear displacement than for a free atom.
+ * For a perfectly circular displacement, this lowers the displacement
+ * by: 1/arcsin(arc_length)
+ * and arcsin(x) = 1 + x^2/6 + ...
+ * For sigma2_rel<<1 the displacement distribution is erfc
+ * (exact formula is provided below). For larger sigma, it is clear
+ * that the displacement can't be larger than 2*com_dist.
+ * It turns out that the distribution becomes nearly uniform.
+ * For intermediate sigma2_rel, scaling down sigma with the third
+ * order expansion of arcsin with argument sigma_rel turns out
+ * to give a very good approximation of the distribution and variance.
+ * Even for larger values, the variance is only slightly overestimated.
+ * Note that the most relevant displacements are in the long tail.
+ * This rotation approximation always overestimates the tail (which
+ * runs to infinity, whereas it should be <= 2*com_dist).
+ * Thus we always overestimate the drift and the buffer size.
+ */
+ scale = 1/(1 + sigma2_rel/6);
+ *sigma2_2d = sigma2_rot*scale*scale;
+ }
+ else
+ {
+ /* sigma_2d is set to the maximum given by the scaling above.
+ * For large sigma2 the real displacement distribution is close
+ * to uniform over -2*con_len to 2*com_dist.
+ * Our erfc with sigma_2d=sqrt(1.5)*com_dist (which means the sigma
+ * of the erfc output distribution is con_dist) overestimates
+ * the variance and additionally has a long tail. This means
+ * we have a (safe) overestimation of the drift.
+ */
+ *sigma2_2d = 1.5*com_dist*com_dist;
+ }
+
+ /* The constrained atom also moves (in 3D) with the COM of both atoms */
+ *sigma2_3d = kT_fac/(prop->mass + prop->con_mass);
+}
+
+static void get_atom_sigma2(real kT_fac,
+ const atom_nonbonded_kinetic_prop_t *prop,
+ real *sigma2_2d,
+ real *sigma2_3d)
+{
+ if (prop->bConstr)
+ {
+ /* Complicated constraint calculation in a separate function */
+ constrained_atom_sigma2(kT_fac, prop, sigma2_2d, sigma2_3d);
+ }
+ else
+ {
+ /* Unconstrained atom: trivial */
+ *sigma2_2d = 0;
+ *sigma2_3d = kT_fac/prop->mass;
+ }
+}
+
+static void approx_2dof(real s2, real x, real *shift, real *scale)
+{
+ /* A particle with 1 DOF constrained has 2 DOFs instead of 3.
+ * This code is also used for particles with multiple constraints,
+ * in which case we overestimate the displacement.
+ * The 2DOF distribution is sqrt(pi/2)*erfc(r/(sqrt(2)*s))/(2*s).
+ * We approximate this with scale*Gaussian(s,r+shift),
+ * by matching the distribution value and derivative at x.
+ * This is a tight overestimate for all r>=0 at any s and x.
+ */
+ real ex, er;
+
+ ex = exp(-x*x/(2*s2));
+ er = std::erfc(x/std::sqrt(2*s2));
+
+ *shift = -x + std::sqrt(2*s2/M_PI)*ex/er;
+ *scale = 0.5*M_PI*std::exp(ex*ex/(M_PI*er*er))*er;
+}
+
+static real ener_drift(const verletbuf_atomtype_t *att, int natt,
+ const gmx_ffparams_t *ffp,
+ real kT_fac,
+ real md1_ljd, real d2_ljd, real md3_ljd,
+ real md1_ljr, real d2_ljr, real md3_ljr,
+ real md1_el, real d2_el,
+ real r_buffer,
+ real rlist, real boxvol)
+{
+ /* Erfc(8)=1e-29, use this limit so we have some space for arithmetic
+ * on the result when using float precision.
+ */
+ const real erfc_arg_max = 8.0;
+
+ double drift_tot, pot1, pot2, pot3, pot;
+ int i, j;
+ real s2i_2d, s2i_3d, s2j_2d, s2j_3d, s2, s;
+ int ti, tj;
+ real md1, d2, md3;
+ real sc_fac, rsh, rsh2;
+ double c_exp, c_erfc;
+
+ drift_tot = 0;
+
+ /* Loop over the different atom type pairs */
+ for (i = 0; i < natt; i++)
+ {
+ get_atom_sigma2(kT_fac, &att[i].prop, &s2i_2d, &s2i_3d);
+ ti = att[i].prop.type;
+
+ for (j = i; j < natt; j++)
+ {
+ get_atom_sigma2(kT_fac, &att[j].prop, &s2j_2d, &s2j_3d);
+ tj = att[j].prop.type;
+
+ /* Add up the up to four independent variances */
+ s2 = s2i_2d + s2i_3d + s2j_2d + s2j_3d;
+
+ /* Note that attractive and repulsive potentials for individual
+ * pairs will partially cancel.
+ */
+ /* -dV/dr at the cut-off for LJ + Coulomb */
+ md1 =
+ md1_ljd*ffp->iparams[ti*ffp->atnr+tj].lj.c6 +
+ md1_ljr*ffp->iparams[ti*ffp->atnr+tj].lj.c12 +
+ md1_el*att[i].prop.q*att[j].prop.q;
+
+ /* d2V/dr2 at the cut-off for LJ + Coulomb */
+ d2 =
+ d2_ljd*ffp->iparams[ti*ffp->atnr+tj].lj.c6 +
+ d2_ljr*ffp->iparams[ti*ffp->atnr+tj].lj.c12 +
+ d2_el*att[i].prop.q*att[j].prop.q;
+
+ /* -d3V/dr3 at the cut-off for LJ, we neglect Coulomb */
+ md3 =
+ md3_ljd*ffp->iparams[ti*ffp->atnr+tj].lj.c6 +
+ md3_ljr*ffp->iparams[ti*ffp->atnr+tj].lj.c12;
+
+ rsh = r_buffer;
+ sc_fac = 1.0;
+
+ if (rsh*rsh > 2*s2*erfc_arg_max*erfc_arg_max)
+ {
+ /* Erfc might run out of float and become 0, somewhat before
+ * c_exp becomes 0. To avoid this and to avoid NaN in
+ * approx_2dof, we set both c_expc and c_erfc to zero.
+ * In any relevant case this has no effect on the results,
+ * since c_exp < 6e-29, so the displacement is completely
+ * negligible for such atom pairs (and an overestimate).
+ * In nearly all use cases, there will be other atom
+ * pairs that contribute much more to the total, so zeroing
+ * this particular contribution has no effect at all.
+ */
+ c_exp = 0;
+ c_erfc = 0;
+ }
+ else
+ {
+ /* For constraints: adapt r and scaling for the Gaussian */
+ if (att[i].prop.bConstr)
+ {
+ real sh, sc;
+
+ approx_2dof(s2i_2d, r_buffer*s2i_2d/s2, &sh, &sc);
+ rsh += sh;
+ sc_fac *= sc;
+ }
+ if (att[j].prop.bConstr)
+ {
+ real sh, sc;
+
+ approx_2dof(s2j_2d, r_buffer*s2j_2d/s2, &sh, &sc);
+ rsh += sh;
+ sc_fac *= sc;
+ }
+
+ /* Exact contribution of an atom pair with Gaussian displacement
+ * with sigma s to the energy drift for a potential with
+ * derivative -md and second derivative dd at the cut-off.
+ * The only catch is that for potentials that change sign
+ * near the cut-off there could be an unlucky compensation
+ * of positive and negative energy drift.
+ * Such potentials are extremely rare though.
+ *
+ * Note that pot has unit energy*length, as the linear
+ * atom density still needs to be put in.
+ */
+ c_exp = std::exp(-rsh*rsh/(2*s2))/std::sqrt(2*M_PI);
+ c_erfc = 0.5*std::erfc(rsh/(std::sqrt(2*s2)));
+ }
+ s = std::sqrt(s2);
+ rsh2 = rsh*rsh;
+
+ pot1 = sc_fac*
+ md1/2*((rsh2 + s2)*c_erfc - rsh*s*c_exp);
+ pot2 = sc_fac*
+ d2/6*(s*(rsh2 + 2*s2)*c_exp - rsh*(rsh2 + 3*s2)*c_erfc);
+ pot3 = sc_fac*
+ md3/24*((rsh2*rsh2 + 6*rsh2*s2 + 3*s2*s2)*c_erfc - rsh*s*(rsh2 + 5*s2)*c_exp);
+ pot = pot1 + pot2 + pot3;
+
+ if (gmx_debug_at)
+ {
+ fprintf(debug, "n %d %d d s %.3f %.3f %.3f %.3f con %d -d1 %8.1e d2 %8.1e -d3 %8.1e pot1 %8.1e pot2 %8.1e pot3 %8.1e pot %8.1e\n",
+ att[i].n, att[j].n,
+ std::sqrt(s2i_2d), std::sqrt(s2i_3d),
+ std::sqrt(s2j_2d), std::sqrt(s2j_3d),
+ att[i].prop.bConstr+att[j].prop.bConstr,
+ md1, d2, md3,
+ pot1, pot2, pot3, pot);
+ }
+
+ /* Multiply by the number of atom pairs */
+ if (j == i)
+ {
+ pot *= (double)att[i].n*(att[i].n - 1)/2;
+ }
+ else
+ {
+ pot *= (double)att[i].n*att[j].n;
+ }
+ /* We need the line density to get the energy drift of the system.
+ * The effective average r^2 is close to (rlist+sigma)^2.
+ */
+ pot *= 4*M_PI*gmx::square(rlist + s)/boxvol;
+
+ /* Add the unsigned drift to avoid cancellation of errors */
+ drift_tot += std::abs(pot);
+ }
+ }
+
+ return drift_tot;
+}
+
+static real surface_frac(int cluster_size, real particle_distance, real rlist)
+{
+ real d, area_rel;
+
+ if (rlist < 0.5*particle_distance)
+ {
+ /* We have non overlapping spheres */
+ return 1.0;
+ }
+
+ /* Half the inter-particle distance relative to rlist */
+ d = 0.5*particle_distance/rlist;
+
+ /* Determine the area of the surface at distance rlist to the closest
+ * particle, relative to surface of a sphere of radius rlist.
+ * The formulas below assume close to cubic cells for the pair search grid,
+ * which the pair search code tries to achieve.
+ * Note that in practice particle distances will not be delta distributed,
+ * but have some spread, often involving shorter distances,
+ * as e.g. O-H bonds in a water molecule. Thus the estimates below will
+ * usually be slightly too high and thus conservative.
+ */
+ switch (cluster_size)
+ {
+ case 1:
+ /* One particle: trivial */
+ area_rel = 1.0;
+ break;
+ case 2:
+ /* Two particles: two spheres at fractional distance 2*a */
+ area_rel = 1.0 + d;
+ break;
+ case 4:
+ /* We assume a perfect, symmetric tetrahedron geometry.
+ * The surface around a tetrahedron is too complex for a full
+ * analytical solution, so we use a Taylor expansion.
+ */
+ area_rel = (1.0 + 1/M_PI*(6*std::acos(1/std::sqrt(3))*d +
+ std::sqrt(3)*d*d*(1.0 +
+ 5.0/18.0*d*d +
+ 7.0/45.0*d*d*d*d +
+ 83.0/756.0*d*d*d*d*d*d)));
+ break;
+ default:
+ gmx_incons("surface_frac called with unsupported cluster_size");
+ area_rel = 1.0;
+ }
+
+ return area_rel/cluster_size;
+}
+
+/* Returns the negative of the third derivative of a potential r^-p
+ * with a force-switch function, evaluated at the cut-off rc.
+ */
+static real md3_force_switch(real p, real rswitch, real rc)
+{
+ /* The switched force function is:
+ * p*r^-(p+1) + a*(r - rswitch)^2 + b*(r - rswitch)^3
+ */
+ real a, b;
+ real md3_pot, md3_sw;
+
+ a = -((p + 4)*rc - (p + 1)*rswitch)/(pow(rc, p+2)*gmx::square(rc-rswitch));
+ b = ((p + 3)*rc - (p + 1)*rswitch)/(pow(rc, p+2)*gmx::power3(rc-rswitch));
+
+ md3_pot = (p + 2)*(p + 1)*p*pow(rc, p+3);
+ md3_sw = 2*a + 6*b*(rc - rswitch);
+
+ return md3_pot + md3_sw;
+}
+
+void calc_verlet_buffer_size(const gmx_mtop_t *mtop, real boxvol,
+ const t_inputrec *ir,
+ real reference_temperature,
+ const verletbuf_list_setup_t *list_setup,
+ int *n_nonlin_vsite,
+ real *rlist)
+{
+ double resolution;
+ char *env;
+
+ real particle_distance;
+ real nb_clust_frac_pairs_not_in_list_at_cutoff;
+
+ verletbuf_atomtype_t *att = NULL;
+ int natt = -1, i;
+ double reppow;
+ real md1_ljd, d2_ljd, md3_ljd;
+ real md1_ljr, d2_ljr, md3_ljr;
+ real md1_el, d2_el;
+ real elfac;
+ real kT_fac, mass_min;
+ int ib0, ib1, ib;
+ real rb, rl;
+ real drift;
+
++ if (!EI_DYNAMICS(ir->eI))
++ {
++ gmx_incons("Can only determine the Verlet buffer size for integrators that perform dynamics");
++ }
++ if (ir->verletbuf_tol <= 0)
++ {
++ gmx_incons("The Verlet buffer tolerance needs to be larger than zero");
++ }
++
+ if (reference_temperature < 0)
+ {
+ if (EI_MD(ir->eI) && ir->etc == etcNO)
+ {
+ /* This case should be handled outside calc_verlet_buffer_size */
+ gmx_incons("calc_verlet_buffer_size called with an NVE ensemble and reference_temperature < 0");
+ }
+
+ /* We use the maximum temperature with multiple T-coupl groups.
+ * We could use a per particle temperature, but since particles
+ * interact, this might underestimate the buffer size.
+ */
+ reference_temperature = 0;
+ for (i = 0; i < ir->opts.ngtc; i++)
+ {
+ if (ir->opts.tau_t[i] >= 0)
+ {
+ reference_temperature = std::max(reference_temperature,
+ ir->opts.ref_t[i]);
+ }
+ }
+ }
+
+ /* Resolution of the buffer size */
+ resolution = 0.001;
+
+ env = getenv("GMX_VERLET_BUFFER_RES");
+ if (env != NULL)
+ {
+ sscanf(env, "%lf", &resolution);
+ }
+
+ /* In an atom wise pair-list there would be no pairs in the list
+ * beyond the pair-list cut-off.
+ * However, we use a pair-list of groups vs groups of atoms.
+ * For groups of 4 atoms, the parallelism of SSE instructions, only
+ * 10% of the atoms pairs are not in the list just beyond the cut-off.
+ * As this percentage increases slowly compared to the decrease of the
+ * Gaussian displacement distribution over this range, we can simply
+ * reduce the drift by this fraction.
+ * For larger groups, e.g. of 8 atoms, this fraction will be lower,
+ * so then buffer size will be on the conservative (large) side.
+ *
+ * Note that the formulas used here do not take into account
+ * cancellation of errors which could occur by missing both
+ * attractive and repulsive interactions.
+ *
+ * The only major assumption is homogeneous particle distribution.
+ * For an inhomogeneous system, such as a liquid-vapor system,
+ * the buffer will be underestimated. The actual energy drift
+ * will be higher by the factor: local/homogeneous particle density.
+ *
+ * The results of this estimate have been checked againt simulations.
+ * In most cases the real drift differs by less than a factor 2.
+ */
+
+ /* Worst case assumption: HCP packing of particles gives largest distance */
+ particle_distance = std::cbrt(boxvol*std::sqrt(2)/mtop->natoms);
+
+ get_verlet_buffer_atomtypes(mtop, &att, &natt, n_nonlin_vsite);
+ assert(att != NULL && natt >= 0);
+
+ if (debug)
+ {
+ fprintf(debug, "particle distance assuming HCP packing: %f nm\n",
+ particle_distance);
+ fprintf(debug, "energy drift atom types: %d\n", natt);
+ }
+
+ reppow = mtop->ffparams.reppow;
+ md1_ljd = 0;
+ d2_ljd = 0;
+ md3_ljd = 0;
+ md1_ljr = 0;
+ d2_ljr = 0;
+ md3_ljr = 0;
+ if (ir->vdwtype == evdwCUT)
+ {
+ real sw_range, md3_pswf;
+
+ switch (ir->vdw_modifier)
+ {
+ case eintmodNONE:
+ case eintmodPOTSHIFT:
+ /* -dV/dr of -r^-6 and r^-reppow */
+ md1_ljd = -6/(ir->rvdw*gmx::power6(ir->rvdw));
+ md1_ljr = reppow*pow(ir->rvdw, -(reppow+1));
+ /* The contribution of the higher derivatives is negligible */
+ break;
+ case eintmodFORCESWITCH:
+ /* At the cut-off: V=V'=V''=0, so we use only V''' */
+ md3_ljd = -md3_force_switch(6.0, ir->rvdw_switch, ir->rvdw);
+ md3_ljr = md3_force_switch(reppow, ir->rvdw_switch, ir->rvdw);
+ break;
+ case eintmodPOTSWITCH:
+ /* At the cut-off: V=V'=V''=0.
+ * V''' is given by the original potential times
+ * the third derivative of the switch function.
+ */
+ sw_range = ir->rvdw - ir->rvdw_switch;
+ md3_pswf = 60.0/gmx::power3(sw_range);
+
+ md3_ljd = -1.0/gmx::power6(ir->rvdw)*md3_pswf;
+ md3_ljr = pow(ir->rvdw, -reppow)*md3_pswf;
+ break;
+ default:
+ gmx_incons("Unimplemented VdW modifier");
+ }
+ }
+ else if (EVDW_PME(ir->vdwtype))
+ {
+ real b, r, br, br2, br4, br6;
+ b = calc_ewaldcoeff_lj(ir->rvdw, ir->ewald_rtol_lj);
+ r = ir->rvdw;
+ br = b*r;
+ br2 = br*br;
+ br4 = br2*br2;
+ br6 = br4*br2;
+ /* -dV/dr of g(br)*r^-6 [where g(x) = exp(-x^2)(1+x^2+x^4/2), see LJ-PME equations in manual] and r^-reppow */
+ md1_ljd = -std::exp(-br2)*(br6 + 3.0*br4 + 6.0*br2 + 6.0)/(r*gmx::power6(r));
+ md1_ljr = reppow*std::pow(r, -(reppow+1));
+ /* The contribution of the higher derivatives is negligible */
+ }
+ else
+ {
+ gmx_fatal(FARGS, "Energy drift calculation is only implemented for plain cut-off Lennard-Jones interactions");
+ }
+
+ elfac = ONE_4PI_EPS0/ir->epsilon_r;
+
+ /* Determine md=-dV/dr and dd=d^2V/dr^2 */
+ md1_el = 0;
+ if (ir->coulombtype == eelCUT || EEL_RF(ir->coulombtype))
+ {
+ real eps_rf, k_rf;
+
+ if (ir->coulombtype == eelCUT)
+ {
+ eps_rf = 1;
+ k_rf = 0;
+ }
+ else
+ {
+ eps_rf = ir->epsilon_rf/ir->epsilon_r;
+ if (eps_rf != 0)
+ {
+ k_rf = (eps_rf - ir->epsilon_r)/( gmx::power3(ir->rcoulomb) * (2*eps_rf + ir->epsilon_r) );
+ }
+ else
+ {
+ /* epsilon_rf = infinity */
+ k_rf = 0.5/gmx::power3(ir->rcoulomb);
+ }
+ }
+
+ if (eps_rf > 0)
+ {
+ md1_el = elfac*(1.0/gmx::square(ir->rcoulomb) - 2*k_rf*ir->rcoulomb);
+ }
+ d2_el = elfac*(2.0/gmx::power3(ir->rcoulomb) + 2*k_rf);
+ }
+ else if (EEL_PME(ir->coulombtype) || ir->coulombtype == eelEWALD)
+ {
+ real b, rc, br;
+
+ b = calc_ewaldcoeff_q(ir->rcoulomb, ir->ewald_rtol);
+ rc = ir->rcoulomb;
+ br = b*rc;
+ md1_el = elfac*(b*exp(-br*br)*M_2_SQRTPI/rc + std::erfc(br)/(rc*rc));
+ d2_el = elfac/(rc*rc)*(2*b*(1 + br*br)*exp(-br*br)*M_2_SQRTPI + 2*std::erfc(br)/rc);
+ }
+ else
+ {
+ gmx_fatal(FARGS, "Energy drift calculation is only implemented for Reaction-Field and Ewald electrostatics");
+ }
+
+ /* Determine the variance of the atomic displacement
+ * over nstlist-1 steps: kT_fac
+ * For inertial dynamics (not Brownian dynamics) the mass factor
+ * is not included in kT_fac, it is added later.
+ */
+ if (ir->eI == eiBD)
+ {
+ /* Get the displacement distribution from the random component only.
+ * With accurate integration the systematic (force) displacement
+ * should be negligible (unless nstlist is extremely large, which
+ * you wouldn't do anyhow).
+ */
+ kT_fac = 2*BOLTZ*reference_temperature*(ir->nstlist-1)*ir->delta_t;
+ if (ir->bd_fric > 0)
+ {
+ /* This is directly sigma^2 of the displacement */
+ kT_fac /= ir->bd_fric;
+
+ /* Set the masses to 1 as kT_fac is the full sigma^2,
+ * but we divide by m in ener_drift().
+ */
+ for (i = 0; i < natt; i++)
+ {
+ att[i].prop.mass = 1;
+ }
+ }
+ else
+ {
+ real tau_t;
+
+ /* Per group tau_t is not implemented yet, use the maximum */
+ tau_t = ir->opts.tau_t[0];
+ for (i = 1; i < ir->opts.ngtc; i++)
+ {
+ tau_t = std::max(tau_t, ir->opts.tau_t[i]);
+ }
+
+ kT_fac *= tau_t;
+ /* This kT_fac needs to be divided by the mass to get sigma^2 */
+ }
+ }
+ else
+ {
+ kT_fac = BOLTZ*reference_temperature*gmx::square((ir->nstlist-1)*ir->delta_t);
+ }
+
+ mass_min = att[0].prop.mass;
+ for (i = 1; i < natt; i++)
+ {
+ mass_min = std::min(mass_min, att[i].prop.mass);
+ }
+
+ if (debug)
+ {
+ fprintf(debug, "md1_ljd %9.2e d2_ljd %9.2e md3_ljd %9.2e\n", md1_ljd, d2_ljd, md3_ljd);
+ fprintf(debug, "md1_ljr %9.2e d2_ljr %9.2e md3_ljr %9.2e\n", md1_ljr, d2_ljr, md3_ljr);
+ fprintf(debug, "md1_el %9.2e d2_el %9.2e\n", md1_el, d2_el);
+ fprintf(debug, "sqrt(kT_fac) %f\n", std::sqrt(kT_fac));
+ fprintf(debug, "mass_min %f\n", mass_min);
+ }
+
+ /* Search using bisection */
+ ib0 = -1;
+ /* The drift will be neglible at 5 times the max sigma */
+ ib1 = (int)(5*2*std::sqrt(kT_fac/mass_min)/resolution) + 1;
+ while (ib1 - ib0 > 1)
+ {
+ ib = (ib0 + ib1)/2;
+ rb = ib*resolution;
+ rl = std::max(ir->rvdw, ir->rcoulomb) + rb;
+
+ /* Calculate the average energy drift at the last step
+ * of the nstlist steps at which the pair-list is used.
+ */
+ drift = ener_drift(att, natt, &mtop->ffparams,
+ kT_fac,
+ md1_ljd, d2_ljd, md3_ljd,
+ md1_ljr, d2_ljr, md3_ljr,
+ md1_el, d2_el,
+ rb,
+ rl, boxvol);
+
+ /* Correct for the fact that we are using a Ni x Nj particle pair list
+ * and not a 1 x 1 particle pair list. This reduces the drift.
+ */
+ /* We don't have a formula for 8 (yet), use 4 which is conservative */
+ nb_clust_frac_pairs_not_in_list_at_cutoff =
+ surface_frac(std::min(list_setup->cluster_size_i, 4),
+ particle_distance, rl)*
+ surface_frac(std::min(list_setup->cluster_size_j, 4),
+ particle_distance, rl);
+ drift *= nb_clust_frac_pairs_not_in_list_at_cutoff;
+
+ /* Convert the drift to drift per unit time per atom */
+ drift /= ir->nstlist*ir->delta_t*mtop->natoms;
+
+ if (debug)
+ {
+ fprintf(debug, "ib %3d %3d %3d rb %.3f %dx%d fac %.3f drift %.1e\n",
+ ib0, ib, ib1, rb,
+ list_setup->cluster_size_i, list_setup->cluster_size_j,
+ nb_clust_frac_pairs_not_in_list_at_cutoff,
+ drift);
+ }
+
+ if (std::abs(drift) > ir->verletbuf_tol)
+ {
+ ib0 = ib;
+ }
+ else
+ {
+ ib1 = ib;
+ }
+ }
+
+ sfree(att);
+
+ *rlist = std::max(ir->rvdw, ir->rcoulomb) + ib1*resolution;
+}
}
/* Construct the coupling coefficient matrix blmf */
- int th, ntriangle = 0, ncc_triangle = 0;
- #pragma omp parallel for reduction(+: ntriangle, ncc_triangle) num_threads(li->ntask) schedule(static)
+ int th, ntriangle = 0, ncc_triangle = 0, nCrossTaskTriangles = 0;
+ #pragma omp parallel for reduction(+: ntriangle, ncc_triangle, nCrossTaskTriangles) num_threads(li->ntask) schedule(static)
for (th = 0; th < li->ntask; th++)
{
- set_lincs_matrix_task(li, &li->task[th], invmass,
- &ncc_triangle, &nCrossTaskTriangles);
- ntriangle = li->task[th].ntriangle;
+ try
+ {
- set_lincs_matrix_task(li, &li->task[th], invmass, &ncc_triangle);
++ set_lincs_matrix_task(li, &li->task[th], invmass,
++ &ncc_triangle, &nCrossTaskTriangles);
+ ntriangle = li->task[th].ntriangle;
+ }
+ GMX_CATCH_ALL_AND_EXIT_WITH_FATAL_ERROR;
}
li->ntriangle = ntriangle;
li->ncc_triangle = ncc_triangle;
#pragma omp parallel for num_threads(nth) schedule(static)
for (th = 0; th < nth; th++)
{
- int start_th, end_th;
-
- if (th > 0)
+ try
{
- clear_mat(constr->vir_r_m_dr_th[th]);
+ int start_th, end_th;
- constr->settle_error[th] = -1;
- }
+ if (th > 0)
+ {
+ clear_mat(constr->vir_r_m_dr_th[th]);
+
- start_th = (nsettle* th )/nth;
- end_th = (nsettle*(th+1))/nth;
- if (start_th >= 0 && end_th - start_th > 0)
- {
- csettle(constr->settled,
- end_th-start_th,
- settle->iatoms+start_th*(1+NRAL(F_SETTLE)),
- pbc_null,
- x[0], xprime[0],
- invdt, v ? v[0] : NULL, calcvir_atom_end,
- th == 0 ? vir_r_m_dr : constr->vir_r_m_dr_th[th],
- th == 0 ? &settle_error : &constr->settle_error[th]);
++ constr->settle_error[th] = -1;
+ }
+
+ start_th = (nsettle* th )/nth;
+ end_th = (nsettle*(th+1))/nth;
+ if (start_th >= 0 && end_th - start_th > 0)
+ {
+ csettle(constr->settled,
+ end_th-start_th,
+ settle->iatoms+start_th*(1+NRAL(F_SETTLE)),
+ pbc_null,
+ x[0], xprime[0],
+ invdt, v ? v[0] : NULL, calcvir_atom_end,
+ th == 0 ? vir_r_m_dr : constr->vir_r_m_dr_th[th],
+ th == 0 ? &settle_error : &constr->settle_error[th]);
+ }
}
+ GMX_CATCH_ALL_AND_EXIT_WITH_FATAL_ERROR;
}
inc_nrnb(nrnb, eNR_SETTLE, nsettle);
if (v != NULL)
--- /dev/null
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 2012,2013,2014,2015,2016, 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 "gmxpre.h"
+
+#include "nbnxn_search.h"
+
+#include "config.h"
+
+#include <assert.h>
+#include <string.h>
+
+#include <cmath>
+
+#include <algorithm>
+
+#include "gromacs/domdec/domdec_struct.h"
+#include "gromacs/gmxlib/nrnb.h"
+#include "gromacs/math/functions.h"
+#include "gromacs/math/utilities.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/mdlib/gmx_omp_nthreads.h"
+#include "gromacs/mdlib/nb_verlet.h"
+#include "gromacs/mdlib/nbnxn_atomdata.h"
+#include "gromacs/mdlib/nbnxn_consts.h"
+#include "gromacs/mdlib/nbnxn_grid.h"
+#include "gromacs/mdlib/nbnxn_internal.h"
+#include "gromacs/mdlib/nbnxn_simd.h"
+#include "gromacs/mdlib/nbnxn_util.h"
+#include "gromacs/mdlib/ns.h"
+#include "gromacs/mdtypes/group.h"
+#include "gromacs/mdtypes/md_enums.h"
+#include "gromacs/pbcutil/ishift.h"
+#include "gromacs/pbcutil/pbc.h"
+#include "gromacs/simd/simd.h"
+#include "gromacs/simd/vector_operations.h"
+#include "gromacs/utility/exceptions.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/smalloc.h"
+
+using namespace gmx; // TODO: Remove when this file is moved into gmx namespace
+
+#if GMX_SIMD
+
+/* The functions below are macros as they are performance sensitive */
+
+/* 4x4 list, pack=4: no complex conversion required */
+/* i-cluster to j-cluster conversion */
+#define CI_TO_CJ_J4(ci) (ci)
+/* cluster index to coordinate array index conversion */
+#define X_IND_CI_J4(ci) ((ci)*STRIDE_P4)
+#define X_IND_CJ_J4(cj) ((cj)*STRIDE_P4)
+
+/* 4x2 list, pack=4: j-cluster size is half the packing width */
+/* i-cluster to j-cluster conversion */
+#define CI_TO_CJ_J2(ci) ((ci)<<1)
+/* cluster index to coordinate array index conversion */
+#define X_IND_CI_J2(ci) ((ci)*STRIDE_P4)
+#define X_IND_CJ_J2(cj) (((cj)>>1)*STRIDE_P4 + ((cj) & 1)*(PACK_X4>>1))
+
+/* 4x8 list, pack=8: i-cluster size is half the packing width */
+/* i-cluster to j-cluster conversion */
+#define CI_TO_CJ_J8(ci) ((ci)>>1)
+/* cluster index to coordinate array index conversion */
+#define X_IND_CI_J8(ci) (((ci)>>1)*STRIDE_P8 + ((ci) & 1)*(PACK_X8>>1))
+#define X_IND_CJ_J8(cj) ((cj)*STRIDE_P8)
+
+/* The j-cluster size is matched to the SIMD width */
+#if GMX_SIMD_REAL_WIDTH == 2
+#define CI_TO_CJ_SIMD_4XN(ci) CI_TO_CJ_J2(ci)
+#define X_IND_CI_SIMD_4XN(ci) X_IND_CI_J2(ci)
+#define X_IND_CJ_SIMD_4XN(cj) X_IND_CJ_J2(cj)
+#else
+#if GMX_SIMD_REAL_WIDTH == 4
+#define CI_TO_CJ_SIMD_4XN(ci) CI_TO_CJ_J4(ci)
+#define X_IND_CI_SIMD_4XN(ci) X_IND_CI_J4(ci)
+#define X_IND_CJ_SIMD_4XN(cj) X_IND_CJ_J4(cj)
+#else
+#if GMX_SIMD_REAL_WIDTH == 8
+#define CI_TO_CJ_SIMD_4XN(ci) CI_TO_CJ_J8(ci)
+#define X_IND_CI_SIMD_4XN(ci) X_IND_CI_J8(ci)
+#define X_IND_CJ_SIMD_4XN(cj) X_IND_CJ_J8(cj)
+/* Half SIMD with j-cluster size */
+#define CI_TO_CJ_SIMD_2XNN(ci) CI_TO_CJ_J4(ci)
+#define X_IND_CI_SIMD_2XNN(ci) X_IND_CI_J4(ci)
+#define X_IND_CJ_SIMD_2XNN(cj) X_IND_CJ_J4(cj)
+#else
+#if GMX_SIMD_REAL_WIDTH == 16
+#define CI_TO_CJ_SIMD_2XNN(ci) CI_TO_CJ_J8(ci)
+#define X_IND_CI_SIMD_2XNN(ci) X_IND_CI_J8(ci)
+#define X_IND_CJ_SIMD_2XNN(cj) X_IND_CJ_J8(cj)
+#else
+#error "unsupported GMX_SIMD_REAL_WIDTH"
+#endif
+#endif
+#endif
+#endif
+
+#endif // GMX_SIMD
+
+
+/* We shift the i-particles backward for PBC.
+ * This leads to more conditionals than shifting forward.
+ * We do this to get more balanced pair lists.
+ */
+#define NBNXN_SHIFT_BACKWARD
+
+
+static void nbs_cycle_clear(nbnxn_cycle_t *cc)
+{
+ for (int i = 0; i < enbsCCnr; i++)
+ {
+ cc[i].count = 0;
+ cc[i].c = 0;
+ }
+}
+
+static double Mcyc_av(const nbnxn_cycle_t *cc)
+{
+ return (double)cc->c*1e-6/cc->count;
+}
+
+static void nbs_cycle_print(FILE *fp, const nbnxn_search_t nbs)
+{
+ fprintf(fp, "\n");
+ fprintf(fp, "ns %4d grid %4.1f search %4.1f red.f %5.3f",
+ nbs->cc[enbsCCgrid].count,
+ Mcyc_av(&nbs->cc[enbsCCgrid]),
+ Mcyc_av(&nbs->cc[enbsCCsearch]),
+ Mcyc_av(&nbs->cc[enbsCCreducef]));
+
+ if (nbs->nthread_max > 1)
+ {
+ if (nbs->cc[enbsCCcombine].count > 0)
+ {
+ fprintf(fp, " comb %5.2f",
+ Mcyc_av(&nbs->cc[enbsCCcombine]));
+ }
+ fprintf(fp, " s. th");
+ for (int t = 0; t < nbs->nthread_max; t++)
+ {
+ fprintf(fp, " %4.1f",
+ Mcyc_av(&nbs->work[t].cc[enbsCCsearch]));
+ }
+ }
+ fprintf(fp, "\n");
+}
+
+static gmx_inline int ci_to_cj(int na_cj_2log, int ci)
+{
+ switch (na_cj_2log)
+ {
+ case 2: return ci; break;
+ case 1: return (ci<<1); break;
+ case 3: return (ci>>1); break;
+ }
+
+ return 0;
+}
+
+gmx_bool nbnxn_kernel_pairlist_simple(int nb_kernel_type)
+{
+ if (nb_kernel_type == nbnxnkNotSet)
+ {
+ gmx_fatal(FARGS, "Non-bonded kernel type not set for Verlet-style pair-list.");
+ }
+
+ switch (nb_kernel_type)
+ {
+ case nbnxnk8x8x8_GPU:
+ case nbnxnk8x8x8_PlainC:
+ return FALSE;
+
+ case nbnxnk4x4_PlainC:
+ case nbnxnk4xN_SIMD_4xN:
+ case nbnxnk4xN_SIMD_2xNN:
+ return TRUE;
+
+ default:
+ gmx_incons("Invalid nonbonded kernel type passed!");
+ return FALSE;
+ }
+}
+
+/* Initializes a single nbnxn_pairlist_t data structure */
+static void nbnxn_init_pairlist_fep(t_nblist *nl)
+{
+ nl->type = GMX_NBLIST_INTERACTION_FREE_ENERGY;
+ nl->igeometry = GMX_NBLIST_GEOMETRY_PARTICLE_PARTICLE;
+ /* The interaction functions are set in the free energy kernel fuction */
+ nl->ivdw = -1;
+ nl->ivdwmod = -1;
+ nl->ielec = -1;
+ nl->ielecmod = -1;
+
+ nl->maxnri = 0;
+ nl->maxnrj = 0;
+ nl->nri = 0;
+ nl->nrj = 0;
+ nl->iinr = NULL;
+ nl->gid = NULL;
+ nl->shift = NULL;
+ nl->jindex = NULL;
+ nl->jjnr = NULL;
+ nl->excl_fep = NULL;
+
+}
+
+void nbnxn_init_search(nbnxn_search_t * nbs_ptr,
+ ivec *n_dd_cells,
+ struct gmx_domdec_zones_t *zones,
+ gmx_bool bFEP,
+ int nthread_max)
+{
+ nbnxn_search_t nbs;
+ int ngrid;
+
+ snew(nbs, 1);
+ *nbs_ptr = nbs;
+
+ nbs->bFEP = bFEP;
+
+ nbs->DomDec = (n_dd_cells != NULL);
+
+ clear_ivec(nbs->dd_dim);
+ ngrid = 1;
+ if (nbs->DomDec)
+ {
+ nbs->zones = zones;
+
+ for (int d = 0; d < DIM; d++)
+ {
+ if ((*n_dd_cells)[d] > 1)
+ {
+ nbs->dd_dim[d] = 1;
+ /* Each grid matches a DD zone */
+ ngrid *= 2;
+ }
+ }
+ }
+
+ nbnxn_grids_init(nbs, ngrid);
+
+ nbs->cell = NULL;
+ nbs->cell_nalloc = 0;
+ nbs->a = NULL;
+ nbs->a_nalloc = 0;
+
+ nbs->nthread_max = nthread_max;
+
+ /* Initialize the work data structures for each thread */
+ snew(nbs->work, nbs->nthread_max);
+ for (int t = 0; t < nbs->nthread_max; t++)
+ {
+ nbs->work[t].cxy_na = NULL;
+ nbs->work[t].cxy_na_nalloc = 0;
+ nbs->work[t].sort_work = NULL;
+ nbs->work[t].sort_work_nalloc = 0;
+
+ snew(nbs->work[t].nbl_fep, 1);
+ nbnxn_init_pairlist_fep(nbs->work[t].nbl_fep);
+ }
+
+ /* Initialize detailed nbsearch cycle counting */
+ nbs->print_cycles = (getenv("GMX_NBNXN_CYCLE") != 0);
+ nbs->search_count = 0;
+ nbs_cycle_clear(nbs->cc);
+ for (int t = 0; t < nbs->nthread_max; t++)
+ {
+ nbs_cycle_clear(nbs->work[t].cc);
+ }
+}
+
+static void init_buffer_flags(nbnxn_buffer_flags_t *flags,
+ int natoms)
+{
+ flags->nflag = (natoms + NBNXN_BUFFERFLAG_SIZE - 1)/NBNXN_BUFFERFLAG_SIZE;
+ if (flags->nflag > flags->flag_nalloc)
+ {
+ flags->flag_nalloc = over_alloc_large(flags->nflag);
+ srenew(flags->flag, flags->flag_nalloc);
+ }
+ for (int b = 0; b < flags->nflag; b++)
+ {
+ bitmask_clear(&(flags->flag[b]));
+ }
+}
+
+/* Determines the cell range along one dimension that
+ * the bounding box b0 - b1 sees.
+ */
+static void get_cell_range(real b0, real b1,
+ int nc, real c0, real s, real invs,
+ real d2, real r2, int *cf, int *cl)
+{
+ *cf = std::max(static_cast<int>((b0 - c0)*invs), 0);
+
+ while (*cf > 0 && d2 + gmx::square((b0 - c0) - (*cf-1+1)*s) < r2)
+ {
+ (*cf)--;
+ }
+
+ *cl = std::min(static_cast<int>((b1 - c0)*invs), nc-1);
+ while (*cl < nc-1 && d2 + gmx::square((*cl+1)*s - (b1 - c0)) < r2)
+ {
+ (*cl)++;
+ }
+}
+
+/* Reference code calculating the distance^2 between two bounding boxes */
+static float box_dist2(float bx0, float bx1, float by0,
+ float by1, float bz0, float bz1,
+ const nbnxn_bb_t *bb)
+{
+ float d2;
+ float dl, dh, dm, dm0;
+
+ d2 = 0;
+
+ dl = bx0 - bb->upper[BB_X];
+ dh = bb->lower[BB_X] - bx1;
+ dm = std::max(dl, dh);
+ dm0 = std::max(dm, 0.0f);
+ d2 += dm0*dm0;
+
+ dl = by0 - bb->upper[BB_Y];
+ dh = bb->lower[BB_Y] - by1;
+ dm = std::max(dl, dh);
+ dm0 = std::max(dm, 0.0f);
+ d2 += dm0*dm0;
+
+ dl = bz0 - bb->upper[BB_Z];
+ dh = bb->lower[BB_Z] - bz1;
+ dm = std::max(dl, dh);
+ dm0 = std::max(dm, 0.0f);
+ d2 += dm0*dm0;
+
+ return d2;
+}
+
+/* Plain C code calculating the distance^2 between two bounding boxes */
+static float subc_bb_dist2(int si, const nbnxn_bb_t *bb_i_ci,
+ int csj, const nbnxn_bb_t *bb_j_all)
+{
+ const nbnxn_bb_t *bb_i, *bb_j;
+ float d2;
+ float dl, dh, dm, dm0;
+
+ bb_i = bb_i_ci + si;
+ bb_j = bb_j_all + csj;
+
+ d2 = 0;
+
+ dl = bb_i->lower[BB_X] - bb_j->upper[BB_X];
+ dh = bb_j->lower[BB_X] - bb_i->upper[BB_X];
+ dm = std::max(dl, dh);
+ dm0 = std::max(dm, 0.0f);
+ d2 += dm0*dm0;
+
+ dl = bb_i->lower[BB_Y] - bb_j->upper[BB_Y];
+ dh = bb_j->lower[BB_Y] - bb_i->upper[BB_Y];
+ dm = std::max(dl, dh);
+ dm0 = std::max(dm, 0.0f);
+ d2 += dm0*dm0;
+
+ dl = bb_i->lower[BB_Z] - bb_j->upper[BB_Z];
+ dh = bb_j->lower[BB_Z] - bb_i->upper[BB_Z];
+ dm = std::max(dl, dh);
+ dm0 = std::max(dm, 0.0f);
+ d2 += dm0*dm0;
+
+ return d2;
+}
+
+#ifdef NBNXN_SEARCH_BB_SIMD4
+
+/* 4-wide SIMD code for bb distance for bb format xyz0 */
+static float subc_bb_dist2_simd4(int si, const nbnxn_bb_t *bb_i_ci,
+ int csj, const nbnxn_bb_t *bb_j_all)
+{
+ // TODO: During SIMDv2 transition only some archs use namespace (remove when done)
+ using namespace gmx;
+
+ Simd4Float bb_i_S0, bb_i_S1;
+ Simd4Float bb_j_S0, bb_j_S1;
+ Simd4Float dl_S;
+ Simd4Float dh_S;
+ Simd4Float dm_S;
+ Simd4Float dm0_S;
+
+ bb_i_S0 = load4(&bb_i_ci[si].lower[0]);
+ bb_i_S1 = load4(&bb_i_ci[si].upper[0]);
+ bb_j_S0 = load4(&bb_j_all[csj].lower[0]);
+ bb_j_S1 = load4(&bb_j_all[csj].upper[0]);
+
+ dl_S = bb_i_S0 - bb_j_S1;
+ dh_S = bb_j_S0 - bb_i_S1;
+
+ dm_S = max(dl_S, dh_S);
+ dm0_S = max(dm_S, simd4SetZeroF());
+
+ return dotProduct(dm0_S, dm0_S);
+}
+
+/* Calculate bb bounding distances of bb_i[si,...,si+3] and store them in d2 */
+#define SUBC_BB_DIST2_SIMD4_XXXX_INNER(si, bb_i, d2) \
+ { \
+ int shi; \
+ \
+ Simd4Float dx_0, dy_0, dz_0; \
+ Simd4Float dx_1, dy_1, dz_1; \
+ \
+ Simd4Float mx, my, mz; \
+ Simd4Float m0x, m0y, m0z; \
+ \
+ Simd4Float d2x, d2y, d2z; \
+ Simd4Float d2s, d2t; \
+ \
+ shi = si*NNBSBB_D*DIM; \
+ \
+ xi_l = load4(bb_i+shi+0*STRIDE_PBB); \
+ yi_l = load4(bb_i+shi+1*STRIDE_PBB); \
+ zi_l = load4(bb_i+shi+2*STRIDE_PBB); \
+ xi_h = load4(bb_i+shi+3*STRIDE_PBB); \
+ yi_h = load4(bb_i+shi+4*STRIDE_PBB); \
+ zi_h = load4(bb_i+shi+5*STRIDE_PBB); \
+ \
+ dx_0 = xi_l - xj_h; \
+ dy_0 = yi_l - yj_h; \
+ dz_0 = zi_l - zj_h; \
+ \
+ dx_1 = xj_l - xi_h; \
+ dy_1 = yj_l - yi_h; \
+ dz_1 = zj_l - zi_h; \
+ \
+ mx = max(dx_0, dx_1); \
+ my = max(dy_0, dy_1); \
+ mz = max(dz_0, dz_1); \
+ \
+ m0x = max(mx, zero); \
+ m0y = max(my, zero); \
+ m0z = max(mz, zero); \
+ \
+ d2x = m0x * m0x; \
+ d2y = m0y * m0y; \
+ d2z = m0z * m0z; \
+ \
+ d2s = d2x + d2y; \
+ d2t = d2s + d2z; \
+ \
+ store4(d2+si, d2t); \
+ }
+
+/* 4-wide SIMD code for nsi bb distances for bb format xxxxyyyyzzzz */
+static void subc_bb_dist2_simd4_xxxx(const float *bb_j,
+ int nsi, const float *bb_i,
+ float *d2)
+{
+ // TODO: During SIMDv2 transition only some archs use namespace (remove when done)
+ using namespace gmx;
+
+ Simd4Float xj_l, yj_l, zj_l;
+ Simd4Float xj_h, yj_h, zj_h;
+ Simd4Float xi_l, yi_l, zi_l;
+ Simd4Float xi_h, yi_h, zi_h;
+
+ Simd4Float zero;
+
+ zero = setZero();
+
+ xj_l = Simd4Float(bb_j[0*STRIDE_PBB]);
+ yj_l = Simd4Float(bb_j[1*STRIDE_PBB]);
+ zj_l = Simd4Float(bb_j[2*STRIDE_PBB]);
+ xj_h = Simd4Float(bb_j[3*STRIDE_PBB]);
+ yj_h = Simd4Float(bb_j[4*STRIDE_PBB]);
+ zj_h = Simd4Float(bb_j[5*STRIDE_PBB]);
+
+ /* Here we "loop" over si (0,STRIDE_PBB) from 0 to nsi with step STRIDE_PBB.
+ * But as we know the number of iterations is 1 or 2, we unroll manually.
+ */
+ SUBC_BB_DIST2_SIMD4_XXXX_INNER(0, bb_i, d2);
+ if (STRIDE_PBB < nsi)
+ {
+ SUBC_BB_DIST2_SIMD4_XXXX_INNER(STRIDE_PBB, bb_i, d2);
+ }
+}
+
+#endif /* NBNXN_SEARCH_BB_SIMD4 */
+
+
+/* Returns if any atom pair from two clusters is within distance sqrt(rl2) */
+static gmx_inline gmx_bool
+clusterpair_in_range(const nbnxn_list_work_t *work,
+ int si,
+ int csj, int stride, const real *x_j,
+ real rl2)
+{
+#ifndef NBNXN_SEARCH_BB_SIMD4
+
+ /* Plain C version.
+ * All coordinates are stored as xyzxyz...
+ */
+
+ const real *x_i = work->x_ci;
+
+ for (int i = 0; i < nbnxn_gpu_cluster_size; i++)
+ {
+ int i0 = (si*nbnxn_gpu_cluster_size + i)*DIM;
+ for (int j = 0; j < nbnxn_gpu_cluster_size; j++)
+ {
+ int j0 = (csj*nbnxn_gpu_cluster_size + j)*stride;
+
+ real d2 = gmx::square(x_i[i0 ] - x_j[j0 ]) + gmx::square(x_i[i0+1] - x_j[j0+1]) + gmx::square(x_i[i0+2] - x_j[j0+2]);
+
+ if (d2 < rl2)
+ {
+ return TRUE;
+ }
+ }
+ }
+
+ return FALSE;
+
+#else /* !NBNXN_SEARCH_BB_SIMD4 */
+
+ /* 4-wide SIMD version.
+ * A cluster is hard-coded to 8 atoms.
+ * The coordinates x_i are stored as xxxxyyyy..., x_j is stored xyzxyz...
+ * Using 8-wide AVX is not faster on Intel Sandy Bridge.
+ */
+ assert(nbnxn_gpu_cluster_size == 8);
+
+ Simd4Real rc2_S = Simd4Real(rl2);
+
+ const real *x_i = work->x_ci_simd;
+
+ int dim_stride = nbnxn_gpu_cluster_size*DIM;
+ Simd4Real ix_S0 = load4(x_i + si*dim_stride + 0*GMX_SIMD4_WIDTH);
+ Simd4Real iy_S0 = load4(x_i + si*dim_stride + 1*GMX_SIMD4_WIDTH);
+ Simd4Real iz_S0 = load4(x_i + si*dim_stride + 2*GMX_SIMD4_WIDTH);
+ Simd4Real ix_S1 = load4(x_i + si*dim_stride + 3*GMX_SIMD4_WIDTH);
+ Simd4Real iy_S1 = load4(x_i + si*dim_stride + 4*GMX_SIMD4_WIDTH);
+ Simd4Real iz_S1 = load4(x_i + si*dim_stride + 5*GMX_SIMD4_WIDTH);
+
+ /* We loop from the outer to the inner particles to maximize
+ * the chance that we find a pair in range quickly and return.
+ */
+ int j0 = csj*nbnxn_gpu_cluster_size;
+ int j1 = j0 + nbnxn_gpu_cluster_size - 1;
+ while (j0 < j1)
+ {
+ Simd4Real jx0_S, jy0_S, jz0_S;
+ Simd4Real jx1_S, jy1_S, jz1_S;
+
+ Simd4Real dx_S0, dy_S0, dz_S0;
+ Simd4Real dx_S1, dy_S1, dz_S1;
+ Simd4Real dx_S2, dy_S2, dz_S2;
+ Simd4Real dx_S3, dy_S3, dz_S3;
+
+ Simd4Real rsq_S0;
+ Simd4Real rsq_S1;
+ Simd4Real rsq_S2;
+ Simd4Real rsq_S3;
+
+ Simd4Bool wco_S0;
+ Simd4Bool wco_S1;
+ Simd4Bool wco_S2;
+ Simd4Bool wco_S3;
+ Simd4Bool wco_any_S01, wco_any_S23, wco_any_S;
+
+ jx0_S = Simd4Real(x_j[j0*stride+0]);
+ jy0_S = Simd4Real(x_j[j0*stride+1]);
+ jz0_S = Simd4Real(x_j[j0*stride+2]);
+
+ jx1_S = Simd4Real(x_j[j1*stride+0]);
+ jy1_S = Simd4Real(x_j[j1*stride+1]);
+ jz1_S = Simd4Real(x_j[j1*stride+2]);
+
+ /* Calculate distance */
+ dx_S0 = ix_S0 - jx0_S;
+ dy_S0 = iy_S0 - jy0_S;
+ dz_S0 = iz_S0 - jz0_S;
+ dx_S1 = ix_S1 - jx0_S;
+ dy_S1 = iy_S1 - jy0_S;
+ dz_S1 = iz_S1 - jz0_S;
+ dx_S2 = ix_S0 - jx1_S;
+ dy_S2 = iy_S0 - jy1_S;
+ dz_S2 = iz_S0 - jz1_S;
+ dx_S3 = ix_S1 - jx1_S;
+ dy_S3 = iy_S1 - jy1_S;
+ dz_S3 = iz_S1 - jz1_S;
+
+ /* rsq = dx*dx+dy*dy+dz*dz */
+ rsq_S0 = norm2(dx_S0, dy_S0, dz_S0);
+ rsq_S1 = norm2(dx_S1, dy_S1, dz_S1);
+ rsq_S2 = norm2(dx_S2, dy_S2, dz_S2);
+ rsq_S3 = norm2(dx_S3, dy_S3, dz_S3);
+
+ wco_S0 = (rsq_S0 < rc2_S);
+ wco_S1 = (rsq_S1 < rc2_S);
+ wco_S2 = (rsq_S2 < rc2_S);
+ wco_S3 = (rsq_S3 < rc2_S);
+
+ wco_any_S01 = wco_S0 || wco_S1;
+ wco_any_S23 = wco_S2 || wco_S3;
+ wco_any_S = wco_any_S01 || wco_any_S23;
+
+ if (anyTrue(wco_any_S))
+ {
+ return TRUE;
+ }
+
+ j0++;
+ j1--;
+ }
+
+ return FALSE;
+
+#endif /* !NBNXN_SEARCH_BB_SIMD4 */
+}
+
+/* Returns the j sub-cell for index cj_ind */
+static int nbl_cj(const nbnxn_pairlist_t *nbl, int cj_ind)
+{
+ return nbl->cj4[cj_ind/nbnxn_gpu_jgroup_size].cj[cj_ind & (nbnxn_gpu_jgroup_size - 1)];
+}
+
+/* Returns the i-interaction mask of the j sub-cell for index cj_ind */
+static unsigned int nbl_imask0(const nbnxn_pairlist_t *nbl, int cj_ind)
+{
+ return nbl->cj4[cj_ind/nbnxn_gpu_jgroup_size].imei[0].imask;
+}
+
+/* Ensures there is enough space for extra extra exclusion masks */
+static void check_excl_space(nbnxn_pairlist_t *nbl, int extra)
+{
+ if (nbl->nexcl+extra > nbl->excl_nalloc)
+ {
+ nbl->excl_nalloc = over_alloc_small(nbl->nexcl+extra);
+ nbnxn_realloc_void((void **)&nbl->excl,
+ nbl->nexcl*sizeof(*nbl->excl),
+ nbl->excl_nalloc*sizeof(*nbl->excl),
+ nbl->alloc, nbl->free);
+ }
+}
+
+/* Ensures there is enough space for ncell extra j-cells in the list */
+static void check_cell_list_space_simple(nbnxn_pairlist_t *nbl,
+ int ncell)
+{
+ int cj_max;
+
+ cj_max = nbl->ncj + ncell;
+
+ if (cj_max > nbl->cj_nalloc)
+ {
+ nbl->cj_nalloc = over_alloc_small(cj_max);
+ nbnxn_realloc_void((void **)&nbl->cj,
+ nbl->ncj*sizeof(*nbl->cj),
+ nbl->cj_nalloc*sizeof(*nbl->cj),
+ nbl->alloc, nbl->free);
+ }
+}
+
+/* Ensures there is enough space for ncell extra j-clusters in the list */
+static void check_cell_list_space_supersub(nbnxn_pairlist_t *nbl,
+ int ncell)
+{
+ int ncj4_max, w;
+
+ /* We can have maximally nsupercell*gpu_ncluster_per_cell sj lists */
+ /* We can store 4 j-subcell - i-supercell pairs in one struct.
+ * since we round down, we need one extra entry.
+ */
+ ncj4_max = ((nbl->work->cj_ind + ncell*gpu_ncluster_per_cell + nbnxn_gpu_jgroup_size - 1)/nbnxn_gpu_jgroup_size);
+
+ if (ncj4_max > nbl->cj4_nalloc)
+ {
+ nbl->cj4_nalloc = over_alloc_small(ncj4_max);
+ nbnxn_realloc_void((void **)&nbl->cj4,
+ nbl->work->cj4_init*sizeof(*nbl->cj4),
+ nbl->cj4_nalloc*sizeof(*nbl->cj4),
+ nbl->alloc, nbl->free);
+ }
+
+ if (ncj4_max > nbl->work->cj4_init)
+ {
+ for (int j4 = nbl->work->cj4_init; j4 < ncj4_max; j4++)
+ {
+ /* No i-subcells and no excl's in the list initially */
+ for (w = 0; w < nbnxn_gpu_clusterpair_split; w++)
+ {
+ nbl->cj4[j4].imei[w].imask = 0U;
+ nbl->cj4[j4].imei[w].excl_ind = 0;
+
+ }
+ }
+ nbl->work->cj4_init = ncj4_max;
+ }
+}
+
+/* Set all excl masks for one GPU warp no exclusions */
+static void set_no_excls(nbnxn_excl_t *excl)
+{
+ for (int t = 0; t < nbnxn_gpu_excl_size; t++)
+ {
+ /* Turn all interaction bits on */
+ excl->pair[t] = NBNXN_INTERACTION_MASK_ALL;
+ }
+}
+
+/* Initializes a single nbnxn_pairlist_t data structure */
+static void nbnxn_init_pairlist(nbnxn_pairlist_t *nbl,
+ gmx_bool bSimple,
+ nbnxn_alloc_t *alloc,
+ nbnxn_free_t *free)
+{
+ if (alloc == NULL)
+ {
+ nbl->alloc = nbnxn_alloc_aligned;
+ }
+ else
+ {
+ nbl->alloc = alloc;
+ }
+ if (free == NULL)
+ {
+ nbl->free = nbnxn_free_aligned;
+ }
+ else
+ {
+ nbl->free = free;
+ }
+
+ nbl->bSimple = bSimple;
+ nbl->na_sc = 0;
+ nbl->na_ci = 0;
+ nbl->na_cj = 0;
+ nbl->nci = 0;
+ nbl->ci = NULL;
+ nbl->ci_nalloc = 0;
++ nbl->nsci = 0;
++ nbl->sci = NULL;
++ nbl->sci_nalloc = 0;
+ nbl->ncj = 0;
+ nbl->cj = NULL;
+ nbl->cj_nalloc = 0;
+ nbl->ncj4 = 0;
+ /* We need one element extra in sj, so alloc initially with 1 */
+ nbl->cj4_nalloc = 0;
+ nbl->cj4 = NULL;
+ nbl->nci_tot = 0;
+
+ if (!nbl->bSimple)
+ {
+ GMX_ASSERT(nbnxn_gpu_ncluster_per_supercluster == gpu_ncluster_per_cell, "The search code assumes that the a super-cluster matches a search grid cell");
+
+ GMX_ASSERT(sizeof(nbl->cj4[0].imei[0].imask)*8 >= nbnxn_gpu_jgroup_size*gpu_ncluster_per_cell, "The i super-cluster cluster interaction mask does not contain a sufficient number of bits");
+ GMX_ASSERT(sizeof(nbl->excl[0])*8 >= nbnxn_gpu_jgroup_size*gpu_ncluster_per_cell, "The GPU exclusion mask does not contain a sufficient number of bits");
+
+ nbl->excl = NULL;
+ nbl->excl_nalloc = 0;
+ nbl->nexcl = 0;
+ check_excl_space(nbl, 1);
+ nbl->nexcl = 1;
+ set_no_excls(&nbl->excl[0]);
+ }
+
+ snew(nbl->work, 1);
+ if (nbl->bSimple)
+ {
+ snew_aligned(nbl->work->bb_ci, 1, NBNXN_SEARCH_BB_MEM_ALIGN);
+ }
+ else
+ {
+#ifdef NBNXN_BBXXXX
+ snew_aligned(nbl->work->pbb_ci, gpu_ncluster_per_cell/STRIDE_PBB*NNBSBB_XXXX, NBNXN_SEARCH_BB_MEM_ALIGN);
+#else
+ snew_aligned(nbl->work->bb_ci, gpu_ncluster_per_cell, NBNXN_SEARCH_BB_MEM_ALIGN);
+#endif
+ }
+ int gpu_clusterpair_nc = gpu_ncluster_per_cell*nbnxn_gpu_cluster_size*DIM;
+ snew(nbl->work->x_ci, gpu_clusterpair_nc);
+#if GMX_SIMD
+ snew_aligned(nbl->work->x_ci_simd,
+ std::max(NBNXN_CPU_CLUSTER_I_SIZE*DIM*GMX_SIMD_REAL_WIDTH,
+ gpu_clusterpair_nc),
+ GMX_SIMD_REAL_WIDTH);
+#endif
+ snew_aligned(nbl->work->d2, gpu_ncluster_per_cell, NBNXN_SEARCH_BB_MEM_ALIGN);
+
+ nbl->work->sort = NULL;
+ nbl->work->sort_nalloc = 0;
+ nbl->work->sci_sort = NULL;
+ nbl->work->sci_sort_nalloc = 0;
+}
+
+void nbnxn_init_pairlist_set(nbnxn_pairlist_set_t *nbl_list,
+ gmx_bool bSimple, gmx_bool bCombined,
+ nbnxn_alloc_t *alloc,
+ nbnxn_free_t *free)
+{
+ nbl_list->bSimple = bSimple;
+ nbl_list->bCombined = bCombined;
+
+ nbl_list->nnbl = gmx_omp_nthreads_get(emntNonbonded);
+
+ if (!nbl_list->bCombined &&
+ nbl_list->nnbl > NBNXN_BUFFERFLAG_MAX_THREADS)
+ {
+ gmx_fatal(FARGS, "%d OpenMP threads were requested. Since the non-bonded force buffer reduction is prohibitively slow with more than %d threads, we do not allow this. Use %d or less OpenMP threads.",
+ nbl_list->nnbl, NBNXN_BUFFERFLAG_MAX_THREADS, NBNXN_BUFFERFLAG_MAX_THREADS);
+ }
+
+ snew(nbl_list->nbl, nbl_list->nnbl);
+ snew(nbl_list->nbl_fep, nbl_list->nnbl);
+ /* Execute in order to avoid memory interleaving between threads */
+#pragma omp parallel for num_threads(nbl_list->nnbl) schedule(static)
+ for (int i = 0; i < nbl_list->nnbl; i++)
+ {
+ try
+ {
+ /* Allocate the nblist data structure locally on each thread
+ * to optimize memory access for NUMA architectures.
+ */
+ snew(nbl_list->nbl[i], 1);
+
+ /* Only list 0 is used on the GPU, use normal allocation for i>0 */
+ if (i == 0)
+ {
+ nbnxn_init_pairlist(nbl_list->nbl[i], nbl_list->bSimple, alloc, free);
+ }
+ else
+ {
+ nbnxn_init_pairlist(nbl_list->nbl[i], nbl_list->bSimple, NULL, NULL);
+ }
+
+ snew(nbl_list->nbl_fep[i], 1);
+ nbnxn_init_pairlist_fep(nbl_list->nbl_fep[i]);
+ }
+ GMX_CATCH_ALL_AND_EXIT_WITH_FATAL_ERROR;
+ }
+}
+
+/* Print statistics of a pair list, used for debug output */
+static void print_nblist_statistics_simple(FILE *fp, const nbnxn_pairlist_t *nbl,
+ const nbnxn_search_t nbs, real rl)
+{
+ const nbnxn_grid_t *grid;
+ int cs[SHIFTS];
+ int npexcl;
+
+ /* This code only produces correct statistics with domain decomposition */
+ grid = &nbs->grid[0];
+
+ fprintf(fp, "nbl nci %d ncj %d\n",
+ nbl->nci, nbl->ncj);
+ fprintf(fp, "nbl na_sc %d rl %g ncp %d per cell %.1f atoms %.1f ratio %.2f\n",
+ nbl->na_sc, rl, nbl->ncj, nbl->ncj/(double)grid->nc,
+ nbl->ncj/(double)grid->nc*grid->na_sc,
+ nbl->ncj/(double)grid->nc*grid->na_sc/(0.5*4.0/3.0*M_PI*rl*rl*rl*grid->nc*grid->na_sc/(grid->size[XX]*grid->size[YY]*grid->size[ZZ])));
+
+ fprintf(fp, "nbl average j cell list length %.1f\n",
+ 0.25*nbl->ncj/(double)std::max(nbl->nci, 1));
+
+ for (int s = 0; s < SHIFTS; s++)
+ {
+ cs[s] = 0;
+ }
+ npexcl = 0;
+ for (int i = 0; i < nbl->nci; i++)
+ {
+ cs[nbl->ci[i].shift & NBNXN_CI_SHIFT] +=
+ nbl->ci[i].cj_ind_end - nbl->ci[i].cj_ind_start;
+
+ int j = nbl->ci[i].cj_ind_start;
+ while (j < nbl->ci[i].cj_ind_end &&
+ nbl->cj[j].excl != NBNXN_INTERACTION_MASK_ALL)
+ {
+ npexcl++;
+ j++;
+ }
+ }
+ fprintf(fp, "nbl cell pairs, total: %d excl: %d %.1f%%\n",
+ nbl->ncj, npexcl, 100*npexcl/(double)std::max(nbl->ncj, 1));
+ for (int s = 0; s < SHIFTS; s++)
+ {
+ if (cs[s] > 0)
+ {
+ fprintf(fp, "nbl shift %2d ncj %3d\n", s, cs[s]);
+ }
+ }
+}
+
+/* Print statistics of a pair lists, used for debug output */
+static void print_nblist_statistics_supersub(FILE *fp, const nbnxn_pairlist_t *nbl,
+ const nbnxn_search_t nbs, real rl)
+{
+ const nbnxn_grid_t *grid;
+ int b;
+ int c[gpu_ncluster_per_cell + 1];
+ double sum_nsp, sum_nsp2;
+ int nsp_max;
+
+ /* This code only produces correct statistics with domain decomposition */
+ grid = &nbs->grid[0];
+
+ fprintf(fp, "nbl nsci %d ncj4 %d nsi %d excl4 %d\n",
+ nbl->nsci, nbl->ncj4, nbl->nci_tot, nbl->nexcl);
+ fprintf(fp, "nbl na_c %d rl %g ncp %d per cell %.1f atoms %.1f ratio %.2f\n",
+ nbl->na_ci, rl, nbl->nci_tot, nbl->nci_tot/(double)grid->nsubc_tot,
+ nbl->nci_tot/(double)grid->nsubc_tot*grid->na_c,
+ nbl->nci_tot/(double)grid->nsubc_tot*grid->na_c/(0.5*4.0/3.0*M_PI*rl*rl*rl*grid->nsubc_tot*grid->na_c/(grid->size[XX]*grid->size[YY]*grid->size[ZZ])));
+
+ sum_nsp = 0;
+ sum_nsp2 = 0;
+ nsp_max = 0;
+ for (int si = 0; si <= gpu_ncluster_per_cell; si++)
+ {
+ c[si] = 0;
+ }
+ for (int i = 0; i < nbl->nsci; i++)
+ {
+ int nsp;
+
+ nsp = 0;
+ for (int j4 = nbl->sci[i].cj4_ind_start; j4 < nbl->sci[i].cj4_ind_end; j4++)
+ {
+ for (int j = 0; j < nbnxn_gpu_jgroup_size; j++)
+ {
+ b = 0;
+ for (int si = 0; si < gpu_ncluster_per_cell; si++)
+ {
+ if (nbl->cj4[j4].imei[0].imask & (1U << (j*gpu_ncluster_per_cell + si)))
+ {
+ b++;
+ }
+ }
+ nsp += b;
+ c[b]++;
+ }
+ }
+ sum_nsp += nsp;
+ sum_nsp2 += nsp*nsp;
+ nsp_max = std::max(nsp_max, nsp);
+ }
+ if (nbl->nsci > 0)
+ {
+ sum_nsp /= nbl->nsci;
+ sum_nsp2 /= nbl->nsci;
+ }
+ fprintf(fp, "nbl #cluster-pairs: av %.1f stddev %.1f max %d\n",
+ sum_nsp, std::sqrt(sum_nsp2 - sum_nsp*sum_nsp), nsp_max);
+
+ if (nbl->ncj4 > 0)
+ {
+ for (b = 0; b <= gpu_ncluster_per_cell; b++)
+ {
+ fprintf(fp, "nbl j-list #i-subcell %d %7d %4.1f\n",
+ b, c[b],
+ 100.0*c[b]/(double)(nbl->ncj4*nbnxn_gpu_jgroup_size));
+ }
+ }
+}
+
+/* Returns a pointer to the exclusion mask for cj4-unit cj4, warp warp */
+static void low_get_nbl_exclusions(nbnxn_pairlist_t *nbl, int cj4,
+ int warp, nbnxn_excl_t **excl)
+{
+ if (nbl->cj4[cj4].imei[warp].excl_ind == 0)
+ {
+ /* No exclusions set, make a new list entry */
+ nbl->cj4[cj4].imei[warp].excl_ind = nbl->nexcl;
+ nbl->nexcl++;
+ *excl = &nbl->excl[nbl->cj4[cj4].imei[warp].excl_ind];
+ set_no_excls(*excl);
+ }
+ else
+ {
+ /* We already have some exclusions, new ones can be added to the list */
+ *excl = &nbl->excl[nbl->cj4[cj4].imei[warp].excl_ind];
+ }
+}
+
+/* Returns a pointer to the exclusion mask for cj4-unit cj4, warp warp,
+ * generates a new element and allocates extra memory, if necessary.
+ */
+static void get_nbl_exclusions_1(nbnxn_pairlist_t *nbl, int cj4,
+ int warp, nbnxn_excl_t **excl)
+{
+ if (nbl->cj4[cj4].imei[warp].excl_ind == 0)
+ {
+ /* We need to make a new list entry, check if we have space */
+ check_excl_space(nbl, 1);
+ }
+ low_get_nbl_exclusions(nbl, cj4, warp, excl);
+}
+
+/* Returns pointers to the exclusion masks for cj4-unit cj4 for both warps,
+ * generates a new element and allocates extra memory, if necessary.
+ */
+static void get_nbl_exclusions_2(nbnxn_pairlist_t *nbl, int cj4,
+ nbnxn_excl_t **excl_w0,
+ nbnxn_excl_t **excl_w1)
+{
+ /* Check for space we might need */
+ check_excl_space(nbl, 2);
+
+ low_get_nbl_exclusions(nbl, cj4, 0, excl_w0);
+ low_get_nbl_exclusions(nbl, cj4, 1, excl_w1);
+}
+
+/* Sets the self exclusions i=j and pair exclusions i>j */
+static void set_self_and_newton_excls_supersub(nbnxn_pairlist_t *nbl,
+ int cj4_ind, int sj_offset,
+ int i_cluster_in_cell)
+{
+ nbnxn_excl_t *excl[nbnxn_gpu_clusterpair_split];
+
+ /* Here we only set the set self and double pair exclusions */
+
+ assert(nbnxn_gpu_clusterpair_split == 2);
+
+ get_nbl_exclusions_2(nbl, cj4_ind, &excl[0], &excl[1]);
+
+ /* Only minor < major bits set */
+ for (int ej = 0; ej < nbl->na_ci; ej++)
+ {
+ int w = (ej>>2);
+ for (int ei = ej; ei < nbl->na_ci; ei++)
+ {
+ excl[w]->pair[(ej & (nbnxn_gpu_jgroup_size-1))*nbl->na_ci + ei] &=
+ ~(1U << (sj_offset*gpu_ncluster_per_cell + i_cluster_in_cell));
+ }
+ }
+}
+
+/* Returns a diagonal or off-diagonal interaction mask for plain C lists */
+static unsigned int get_imask(gmx_bool rdiag, int ci, int cj)
+{
+ return (rdiag && ci == cj ? NBNXN_INTERACTION_MASK_DIAG : NBNXN_INTERACTION_MASK_ALL);
+}
+
+/* Returns a diagonal or off-diagonal interaction mask for cj-size=2 */
+static unsigned int get_imask_simd_j2(gmx_bool rdiag, int ci, int cj)
+{
+ return (rdiag && ci*2 == cj ? NBNXN_INTERACTION_MASK_DIAG_J2_0 :
+ (rdiag && ci*2+1 == cj ? NBNXN_INTERACTION_MASK_DIAG_J2_1 :
+ NBNXN_INTERACTION_MASK_ALL));
+}
+
+/* Returns a diagonal or off-diagonal interaction mask for cj-size=4 */
+static unsigned int get_imask_simd_j4(gmx_bool rdiag, int ci, int cj)
+{
+ return (rdiag && ci == cj ? NBNXN_INTERACTION_MASK_DIAG : NBNXN_INTERACTION_MASK_ALL);
+}
+
+/* Returns a diagonal or off-diagonal interaction mask for cj-size=8 */
+static unsigned int get_imask_simd_j8(gmx_bool rdiag, int ci, int cj)
+{
+ return (rdiag && ci == cj*2 ? NBNXN_INTERACTION_MASK_DIAG_J8_0 :
+ (rdiag && ci == cj*2+1 ? NBNXN_INTERACTION_MASK_DIAG_J8_1 :
+ NBNXN_INTERACTION_MASK_ALL));
+}
+
+#if GMX_SIMD
+#if GMX_SIMD_REAL_WIDTH == 2
+#define get_imask_simd_4xn get_imask_simd_j2
+#endif
+#if GMX_SIMD_REAL_WIDTH == 4
+#define get_imask_simd_4xn get_imask_simd_j4
+#endif
+#if GMX_SIMD_REAL_WIDTH == 8
+#define get_imask_simd_4xn get_imask_simd_j8
+#define get_imask_simd_2xnn get_imask_simd_j4
+#endif
+#if GMX_SIMD_REAL_WIDTH == 16
+#define get_imask_simd_2xnn get_imask_simd_j8
+#endif
+#endif
+
+/* Plain C code for making a pair list of cell ci vs cell cjf-cjl.
+ * Checks bounding box distances and possibly atom pair distances.
+ */
+static void make_cluster_list_simple(const nbnxn_grid_t *gridj,
+ nbnxn_pairlist_t *nbl,
+ int ci, int cjf, int cjl,
+ gmx_bool remove_sub_diag,
+ const real *x_j,
+ real rl2, float rbb2,
+ int *ndistc)
+{
+ const nbnxn_bb_t *bb_ci;
+ const real *x_ci;
+
+ gmx_bool InRange;
+ real d2;
+ int cjf_gl, cjl_gl;
+
+ bb_ci = nbl->work->bb_ci;
+ x_ci = nbl->work->x_ci;
+
+ InRange = FALSE;
+ while (!InRange && cjf <= cjl)
+ {
+ d2 = subc_bb_dist2(0, bb_ci, cjf, gridj->bb);
+ *ndistc += 2;
+
+ /* Check if the distance is within the distance where
+ * we use only the bounding box distance rbb,
+ * or within the cut-off and there is at least one atom pair
+ * within the cut-off.
+ */
+ if (d2 < rbb2)
+ {
+ InRange = TRUE;
+ }
+ else if (d2 < rl2)
+ {
+ cjf_gl = gridj->cell0 + cjf;
+ for (int i = 0; i < NBNXN_CPU_CLUSTER_I_SIZE && !InRange; i++)
+ {
+ for (int j = 0; j < NBNXN_CPU_CLUSTER_I_SIZE; j++)
+ {
+ InRange = InRange ||
+ (gmx::square(x_ci[i*STRIDE_XYZ+XX] - x_j[(cjf_gl*NBNXN_CPU_CLUSTER_I_SIZE+j)*STRIDE_XYZ+XX]) +
+ gmx::square(x_ci[i*STRIDE_XYZ+YY] - x_j[(cjf_gl*NBNXN_CPU_CLUSTER_I_SIZE+j)*STRIDE_XYZ+YY]) +
+ gmx::square(x_ci[i*STRIDE_XYZ+ZZ] - x_j[(cjf_gl*NBNXN_CPU_CLUSTER_I_SIZE+j)*STRIDE_XYZ+ZZ]) < rl2);
+ }
+ }
+ *ndistc += NBNXN_CPU_CLUSTER_I_SIZE*NBNXN_CPU_CLUSTER_I_SIZE;
+ }
+ if (!InRange)
+ {
+ cjf++;
+ }
+ }
+ if (!InRange)
+ {
+ return;
+ }
+
+ InRange = FALSE;
+ while (!InRange && cjl > cjf)
+ {
+ d2 = subc_bb_dist2(0, bb_ci, cjl, gridj->bb);
+ *ndistc += 2;
+
+ /* Check if the distance is within the distance where
+ * we use only the bounding box distance rbb,
+ * or within the cut-off and there is at least one atom pair
+ * within the cut-off.
+ */
+ if (d2 < rbb2)
+ {
+ InRange = TRUE;
+ }
+ else if (d2 < rl2)
+ {
+ cjl_gl = gridj->cell0 + cjl;
+ for (int i = 0; i < NBNXN_CPU_CLUSTER_I_SIZE && !InRange; i++)
+ {
+ for (int j = 0; j < NBNXN_CPU_CLUSTER_I_SIZE; j++)
+ {
+ InRange = InRange ||
+ (gmx::square(x_ci[i*STRIDE_XYZ+XX] - x_j[(cjl_gl*NBNXN_CPU_CLUSTER_I_SIZE+j)*STRIDE_XYZ+XX]) +
+ gmx::square(x_ci[i*STRIDE_XYZ+YY] - x_j[(cjl_gl*NBNXN_CPU_CLUSTER_I_SIZE+j)*STRIDE_XYZ+YY]) +
+ gmx::square(x_ci[i*STRIDE_XYZ+ZZ] - x_j[(cjl_gl*NBNXN_CPU_CLUSTER_I_SIZE+j)*STRIDE_XYZ+ZZ]) < rl2);
+ }
+ }
+ *ndistc += NBNXN_CPU_CLUSTER_I_SIZE*NBNXN_CPU_CLUSTER_I_SIZE;
+ }
+ if (!InRange)
+ {
+ cjl--;
+ }
+ }
+
+ if (cjf <= cjl)
+ {
+ for (int cj = cjf; cj <= cjl; cj++)
+ {
+ /* Store cj and the interaction mask */
+ nbl->cj[nbl->ncj].cj = gridj->cell0 + cj;
+ nbl->cj[nbl->ncj].excl = get_imask(remove_sub_diag, ci, cj);
+ nbl->ncj++;
+ }
+ /* Increase the closing index in i super-cell list */
+ nbl->ci[nbl->nci].cj_ind_end = nbl->ncj;
+ }
+}
+
+#ifdef GMX_NBNXN_SIMD_4XN
+#include "gromacs/mdlib/nbnxn_search_simd_4xn.h"
+#endif
+#ifdef GMX_NBNXN_SIMD_2XNN
+#include "gromacs/mdlib/nbnxn_search_simd_2xnn.h"
+#endif
+
+/* Plain C or SIMD4 code for making a pair list of super-cell sci vs scj.
+ * Checks bounding box distances and possibly atom pair distances.
+ */
+static void make_cluster_list_supersub(const nbnxn_grid_t *gridi,
+ const nbnxn_grid_t *gridj,
+ nbnxn_pairlist_t *nbl,
+ int sci, int scj,
+ gmx_bool sci_equals_scj,
+ int stride, const real *x,
+ real rl2, float rbb2,
+ int *ndistc)
+{
+ nbnxn_list_work_t *work = nbl->work;
+
+#ifdef NBNXN_BBXXXX
+ const float *pbb_ci = work->pbb_ci;
+#else
+ const nbnxn_bb_t *bb_ci = work->bb_ci;
+#endif
+
+ const int na_c = nbnxn_gpu_cluster_size;
+ assert(na_c == gridi->na_c);
+ assert(na_c == gridj->na_c);
+
+ /* We generate the pairlist mainly based on bounding-box distances
+ * and do atom pair distance based pruning on the GPU.
+ * Only if a j-group contains a single cluster-pair, we try to prune
+ * that pair based on atom distances on the CPU to avoid empty j-groups.
+ */
+#define PRUNE_LIST_CPU_ONE
+#ifdef PRUNE_LIST_CPU_ONE
+ int ci_last = -1;
+#endif
+
+ float *d2l = work->d2;
+
+ for (int subc = 0; subc < gridj->nsubc[scj]; subc++)
+ {
+ int cj4_ind = nbl->work->cj_ind/nbnxn_gpu_jgroup_size;
+ int cj_offset = nbl->work->cj_ind - cj4_ind*nbnxn_gpu_jgroup_size;
+ nbnxn_cj4_t *cj4 = &nbl->cj4[cj4_ind];
+
+ int cj = scj*gpu_ncluster_per_cell + subc;
+
+ int cj_gl = gridj->cell0*gpu_ncluster_per_cell + cj;
+
+ /* Initialize this j-subcell i-subcell list */
+ cj4->cj[cj_offset] = cj_gl;
+
+ int ci1;
+ if (sci_equals_scj)
+ {
+ ci1 = subc + 1;
+ }
+ else
+ {
+ ci1 = gridi->nsubc[sci];
+ }
+
+#ifdef NBNXN_BBXXXX
+ /* Determine all ci1 bb distances in one call with SIMD4 */
+ subc_bb_dist2_simd4_xxxx(gridj->pbb+(cj>>STRIDE_PBB_2LOG)*NNBSBB_XXXX+(cj & (STRIDE_PBB-1)),
+ ci1, pbb_ci, d2l);
+ *ndistc += na_c*2;
+#endif
+
+ int npair = 0;
+ unsigned int imask = 0;
+ /* We use a fixed upper-bound instead of ci1 to help optimization */
+ for (int ci = 0; ci < gpu_ncluster_per_cell; ci++)
+ {
+ if (ci == ci1)
+ {
+ break;
+ }
+
+#ifndef NBNXN_BBXXXX
+ /* Determine the bb distance between ci and cj */
+ d2l[ci] = subc_bb_dist2(ci, bb_ci, cj, gridj->bb);
+ *ndistc += 2;
+#endif
+ float d2 = d2l[ci];
+
+#ifdef PRUNE_LIST_CPU_ALL
+ /* Check if the distance is within the distance where
+ * we use only the bounding box distance rbb,
+ * or within the cut-off and there is at least one atom pair
+ * within the cut-off. This check is very costly.
+ */
+ *ndistc += na_c*na_c;
+ if (d2 < rbb2 ||
+ (d2 < rl2 &&
+ clusterpair_in_range(work, ci, cj_gl, stride, x, rl2)))
+#else
+ /* Check if the distance between the two bounding boxes
+ * in within the pair-list cut-off.
+ */
+ if (d2 < rl2)
+#endif
+ {
+ /* Flag this i-subcell to be taken into account */
+ imask |= (1U << (cj_offset*gpu_ncluster_per_cell + ci));
+
+#ifdef PRUNE_LIST_CPU_ONE
+ ci_last = ci;
+#endif
+
+ npair++;
+ }
+ }
+
+#ifdef PRUNE_LIST_CPU_ONE
+ /* If we only found 1 pair, check if any atoms are actually
+ * within the cut-off, so we could get rid of it.
+ */
+ if (npair == 1 && d2l[ci_last] >= rbb2 &&
+ !clusterpair_in_range(work, ci_last, cj_gl, stride, x, rl2))
+ {
+ imask &= ~(1U << (cj_offset*gpu_ncluster_per_cell + ci_last));
+ npair--;
+ }
+#endif
+
+ if (npair > 0)
+ {
+ /* We have a useful sj entry, close it now */
+
+ /* Set the exclucions for the ci== sj entry.
+ * Here we don't bother to check if this entry is actually flagged,
+ * as it will nearly always be in the list.
+ */
+ if (sci_equals_scj)
+ {
+ set_self_and_newton_excls_supersub(nbl, cj4_ind, cj_offset, subc);
+ }
+
+ /* Copy the cluster interaction mask to the list */
+ for (int w = 0; w < nbnxn_gpu_clusterpair_split; w++)
+ {
+ cj4->imei[w].imask |= imask;
+ }
+
+ nbl->work->cj_ind++;
+
+ /* Keep the count */
+ nbl->nci_tot += npair;
+
+ /* Increase the closing index in i super-cell list */
+ nbl->sci[nbl->nsci].cj4_ind_end =
+ (nbl->work->cj_ind + nbnxn_gpu_jgroup_size - 1)/nbnxn_gpu_jgroup_size;
+ }
+ }
+}
+
+/* Set all atom-pair exclusions from the topology stored in excl
+ * as masks in the pair-list for simple list i-entry nbl_ci
+ */
+static void set_ci_top_excls(const nbnxn_search_t nbs,
+ nbnxn_pairlist_t *nbl,
+ gmx_bool diagRemoved,
+ int na_ci_2log,
+ int na_cj_2log,
+ const nbnxn_ci_t *nbl_ci,
+ const t_blocka *excl)
+{
+ const int *cell;
+ int ci;
+ int cj_ind_first, cj_ind_last;
+ int cj_first, cj_last;
+ int ndirect;
+ int ai, aj, si, ge, se;
+ int found, cj_ind_0, cj_ind_1, cj_ind_m;
+ int cj_m;
+ int inner_i, inner_e;
+
+ cell = nbs->cell;
+
+ if (nbl_ci->cj_ind_end == nbl_ci->cj_ind_start)
+ {
+ /* Empty list */
+ return;
+ }
+
+ ci = nbl_ci->ci;
+
+ cj_ind_first = nbl_ci->cj_ind_start;
+ cj_ind_last = nbl->ncj - 1;
+
+ cj_first = nbl->cj[cj_ind_first].cj;
+ cj_last = nbl->cj[cj_ind_last].cj;
+
+ /* Determine how many contiguous j-cells we have starting
+ * from the first i-cell. This number can be used to directly
+ * calculate j-cell indices for excluded atoms.
+ */
+ ndirect = 0;
+ if (na_ci_2log == na_cj_2log)
+ {
+ while (cj_ind_first + ndirect <= cj_ind_last &&
+ nbl->cj[cj_ind_first+ndirect].cj == ci + ndirect)
+ {
+ ndirect++;
+ }
+ }
+#ifdef NBNXN_SEARCH_BB_SIMD4
+ else
+ {
+ while (cj_ind_first + ndirect <= cj_ind_last &&
+ nbl->cj[cj_ind_first+ndirect].cj == ci_to_cj(na_cj_2log, ci) + ndirect)
+ {
+ ndirect++;
+ }
+ }
+#endif
+
+ /* Loop over the atoms in the i super-cell */
+ for (int i = 0; i < nbl->na_sc; i++)
+ {
+ ai = nbs->a[ci*nbl->na_sc+i];
+ if (ai >= 0)
+ {
+ si = (i>>na_ci_2log);
+
+ /* Loop over the topology-based exclusions for this i-atom */
+ for (int eind = excl->index[ai]; eind < excl->index[ai+1]; eind++)
+ {
+ aj = excl->a[eind];
+
+ if (aj == ai)
+ {
+ /* The self exclusion are already set, save some time */
+ continue;
+ }
+
+ ge = cell[aj];
+
+ /* Without shifts we only calculate interactions j>i
+ * for one-way pair-lists.
+ */
+ if (diagRemoved && ge <= ci*nbl->na_sc + i)
+ {
+ continue;
+ }
+
+ se = (ge >> na_cj_2log);
+
+ /* Could the cluster se be in our list? */
+ if (se >= cj_first && se <= cj_last)
+ {
+ if (se < cj_first + ndirect)
+ {
+ /* We can calculate cj_ind directly from se */
+ found = cj_ind_first + se - cj_first;
+ }
+ else
+ {
+ /* Search for se using bisection */
+ found = -1;
+ cj_ind_0 = cj_ind_first + ndirect;
+ cj_ind_1 = cj_ind_last + 1;
+ while (found == -1 && cj_ind_0 < cj_ind_1)
+ {
+ cj_ind_m = (cj_ind_0 + cj_ind_1)>>1;
+
+ cj_m = nbl->cj[cj_ind_m].cj;
+
+ if (se == cj_m)
+ {
+ found = cj_ind_m;
+ }
+ else if (se < cj_m)
+ {
+ cj_ind_1 = cj_ind_m;
+ }
+ else
+ {
+ cj_ind_0 = cj_ind_m + 1;
+ }
+ }
+ }
+
+ if (found >= 0)
+ {
+ inner_i = i - (si << na_ci_2log);
+ inner_e = ge - (se << na_cj_2log);
+
+ nbl->cj[found].excl &= ~(1U<<((inner_i<<na_cj_2log) + inner_e));
+ }
+ }
+ }
+ }
+ }
+}
+
+/* Add a new i-entry to the FEP list and copy the i-properties */
+static gmx_inline void fep_list_new_nri_copy(t_nblist *nlist)
+{
+ /* Add a new i-entry */
+ nlist->nri++;
+
+ assert(nlist->nri < nlist->maxnri);
+
+ /* Duplicate the last i-entry, except for jindex, which continues */
+ nlist->iinr[nlist->nri] = nlist->iinr[nlist->nri-1];
+ nlist->shift[nlist->nri] = nlist->shift[nlist->nri-1];
+ nlist->gid[nlist->nri] = nlist->gid[nlist->nri-1];
+ nlist->jindex[nlist->nri] = nlist->nrj;
+}
+
+/* For load balancing of the free-energy lists over threads, we set
+ * the maximum nrj size of an i-entry to 40. This leads to good
+ * load balancing in the worst case scenario of a single perturbed
+ * particle on 16 threads, while not introducing significant overhead.
+ * Note that half of the perturbed pairs will anyhow end up in very small lists,
+ * since non perturbed i-particles will see few perturbed j-particles).
+ */
+const int max_nrj_fep = 40;
+
+/* Exclude the perturbed pairs from the Verlet list. This is only done to avoid
+ * singularities for overlapping particles (0/0), since the charges and
+ * LJ parameters have been zeroed in the nbnxn data structure.
+ * Simultaneously make a group pair list for the perturbed pairs.
+ */
+static void make_fep_list(const nbnxn_search_t nbs,
+ const nbnxn_atomdata_t *nbat,
+ nbnxn_pairlist_t *nbl,
+ gmx_bool bDiagRemoved,
+ nbnxn_ci_t *nbl_ci,
+ const nbnxn_grid_t *gridi,
+ const nbnxn_grid_t *gridj,
+ t_nblist *nlist)
+{
+ int ci, cj_ind_start, cj_ind_end, cja, cjr;
+ int nri_max;
+ int ngid, gid_i = 0, gid_j, gid;
+ int egp_shift, egp_mask;
+ int gid_cj = 0;
+ int ind_i, ind_j, ai, aj;
+ int nri;
+ gmx_bool bFEP_i, bFEP_i_all;
+
+ if (nbl_ci->cj_ind_end == nbl_ci->cj_ind_start)
+ {
+ /* Empty list */
+ return;
+ }
+
+ ci = nbl_ci->ci;
+
+ cj_ind_start = nbl_ci->cj_ind_start;
+ cj_ind_end = nbl_ci->cj_ind_end;
+
+ /* In worst case we have alternating energy groups
+ * and create #atom-pair lists, which means we need the size
+ * of a cluster pair (na_ci*na_cj) times the number of cj's.
+ */
+ nri_max = nbl->na_ci*nbl->na_cj*(cj_ind_end - cj_ind_start);
+ if (nlist->nri + nri_max > nlist->maxnri)
+ {
+ nlist->maxnri = over_alloc_large(nlist->nri + nri_max);
+ reallocate_nblist(nlist);
+ }
+
+ ngid = nbat->nenergrp;
+
+ if (static_cast<std::size_t>(ngid*gridj->na_cj) > sizeof(gid_cj)*8)
+ {
+ gmx_fatal(FARGS, "The Verlet scheme with %dx%d kernels and free-energy only supports up to %d energy groups",
+ gridi->na_c, gridj->na_cj, (sizeof(gid_cj)*8)/gridj->na_cj);
+ }
+
+ egp_shift = nbat->neg_2log;
+ egp_mask = (1<<nbat->neg_2log) - 1;
+
+ /* Loop over the atoms in the i sub-cell */
+ bFEP_i_all = TRUE;
+ for (int i = 0; i < nbl->na_ci; i++)
+ {
+ ind_i = ci*nbl->na_ci + i;
+ ai = nbs->a[ind_i];
+ if (ai >= 0)
+ {
+ nri = nlist->nri;
+ nlist->jindex[nri+1] = nlist->jindex[nri];
+ nlist->iinr[nri] = ai;
+ /* The actual energy group pair index is set later */
+ nlist->gid[nri] = 0;
+ nlist->shift[nri] = nbl_ci->shift & NBNXN_CI_SHIFT;
+
+ bFEP_i = gridi->fep[ci - gridi->cell0] & (1 << i);
+
+ bFEP_i_all = bFEP_i_all && bFEP_i;
+
+ if ((nlist->nrj + cj_ind_end - cj_ind_start)*nbl->na_cj > nlist->maxnrj)
+ {
+ nlist->maxnrj = over_alloc_small((nlist->nrj + cj_ind_end - cj_ind_start)*nbl->na_cj);
+ srenew(nlist->jjnr, nlist->maxnrj);
+ srenew(nlist->excl_fep, nlist->maxnrj);
+ }
+
+ if (ngid > 1)
+ {
+ gid_i = (nbat->energrp[ci] >> (egp_shift*i)) & egp_mask;
+ }
+
+ for (int cj_ind = cj_ind_start; cj_ind < cj_ind_end; cj_ind++)
+ {
+ unsigned int fep_cj;
+
+ cja = nbl->cj[cj_ind].cj;
+
+ if (gridj->na_cj == gridj->na_c)
+ {
+ cjr = cja - gridj->cell0;
+ fep_cj = gridj->fep[cjr];
+ if (ngid > 1)
+ {
+ gid_cj = nbat->energrp[cja];
+ }
+ }
+ else if (2*gridj->na_cj == gridj->na_c)
+ {
+ cjr = cja - gridj->cell0*2;
+ /* Extract half of the ci fep/energrp mask */
+ fep_cj = (gridj->fep[cjr>>1] >> ((cjr&1)*gridj->na_cj)) & ((1<<gridj->na_cj) - 1);
+ if (ngid > 1)
+ {
+ gid_cj = nbat->energrp[cja>>1] >> ((cja&1)*gridj->na_cj*egp_shift) & ((1<<(gridj->na_cj*egp_shift)) - 1);
+ }
+ }
+ else
+ {
+ cjr = cja - (gridj->cell0>>1);
+ /* Combine two ci fep masks/energrp */
+ fep_cj = gridj->fep[cjr*2] + (gridj->fep[cjr*2+1] << gridj->na_c);
+ if (ngid > 1)
+ {
+ gid_cj = nbat->energrp[cja*2] + (nbat->energrp[cja*2+1] << (gridj->na_c*egp_shift));
+ }
+ }
+
+ if (bFEP_i || fep_cj != 0)
+ {
+ for (int j = 0; j < nbl->na_cj; j++)
+ {
+ /* Is this interaction perturbed and not excluded? */
+ ind_j = cja*nbl->na_cj + j;
+ aj = nbs->a[ind_j];
+ if (aj >= 0 &&
+ (bFEP_i || (fep_cj & (1 << j))) &&
+ (!bDiagRemoved || ind_j >= ind_i))
+ {
+ if (ngid > 1)
+ {
+ gid_j = (gid_cj >> (j*egp_shift)) & egp_mask;
+ gid = GID(gid_i, gid_j, ngid);
+
+ if (nlist->nrj > nlist->jindex[nri] &&
+ nlist->gid[nri] != gid)
+ {
+ /* Energy group pair changed: new list */
+ fep_list_new_nri_copy(nlist);
+ nri = nlist->nri;
+ }
+ nlist->gid[nri] = gid;
+ }
+
+ if (nlist->nrj - nlist->jindex[nri] >= max_nrj_fep)
+ {
+ fep_list_new_nri_copy(nlist);
+ nri = nlist->nri;
+ }
+
+ /* Add it to the FEP list */
+ nlist->jjnr[nlist->nrj] = aj;
+ nlist->excl_fep[nlist->nrj] = (nbl->cj[cj_ind].excl >> (i*nbl->na_cj + j)) & 1;
+ nlist->nrj++;
+
+ /* Exclude it from the normal list.
+ * Note that the charge has been set to zero,
+ * but we need to avoid 0/0, as perturbed atoms
+ * can be on top of each other.
+ */
+ nbl->cj[cj_ind].excl &= ~(1U << (i*nbl->na_cj + j));
+ }
+ }
+ }
+ }
+
+ if (nlist->nrj > nlist->jindex[nri])
+ {
+ /* Actually add this new, non-empty, list */
+ nlist->nri++;
+ nlist->jindex[nlist->nri] = nlist->nrj;
+ }
+ }
+ }
+
+ if (bFEP_i_all)
+ {
+ /* All interactions are perturbed, we can skip this entry */
+ nbl_ci->cj_ind_end = cj_ind_start;
+ }
+}
+
+/* Return the index of atom a within a cluster */
+static gmx_inline int cj_mod_cj4(int cj)
+{
+ return cj & (nbnxn_gpu_jgroup_size - 1);
+}
+
+/* Convert a j-cluster to a cj4 group */
+static gmx_inline int cj_to_cj4(int cj)
+{
+ return cj/nbnxn_gpu_jgroup_size;
+}
+
+/* Return the index of an j-atom within a warp */
+static gmx_inline int a_mod_wj(int a)
+{
+ return a & (nbnxn_gpu_cluster_size/nbnxn_gpu_clusterpair_split - 1);
+}
+
+/* As make_fep_list above, but for super/sub lists. */
+static void make_fep_list_supersub(const nbnxn_search_t nbs,
+ const nbnxn_atomdata_t *nbat,
+ nbnxn_pairlist_t *nbl,
+ gmx_bool bDiagRemoved,
+ const nbnxn_sci_t *nbl_sci,
+ real shx,
+ real shy,
+ real shz,
+ real rlist_fep2,
+ const nbnxn_grid_t *gridi,
+ const nbnxn_grid_t *gridj,
+ t_nblist *nlist)
+{
+ int sci, cj4_ind_start, cj4_ind_end, cjr;
+ int nri_max;
+ int c_abs;
+ int ind_i, ind_j, ai, aj;
+ int nri;
+ gmx_bool bFEP_i;
+ real xi, yi, zi;
+ const nbnxn_cj4_t *cj4;
+
+ if (nbl_sci->cj4_ind_end == nbl_sci->cj4_ind_start)
+ {
+ /* Empty list */
+ return;
+ }
+
+ sci = nbl_sci->sci;
+
+ cj4_ind_start = nbl_sci->cj4_ind_start;
+ cj4_ind_end = nbl_sci->cj4_ind_end;
+
+ /* Here we process one super-cell, max #atoms na_sc, versus a list
+ * cj4 entries, each with max nbnxn_gpu_jgroup_size cj's, each
+ * of size na_cj atoms.
+ * On the GPU we don't support energy groups (yet).
+ * So for each of the na_sc i-atoms, we need max one FEP list
+ * for each max_nrj_fep j-atoms.
+ */
+ nri_max = nbl->na_sc*nbl->na_cj*(1 + ((cj4_ind_end - cj4_ind_start)*nbnxn_gpu_jgroup_size)/max_nrj_fep);
+ if (nlist->nri + nri_max > nlist->maxnri)
+ {
+ nlist->maxnri = over_alloc_large(nlist->nri + nri_max);
+ reallocate_nblist(nlist);
+ }
+
+ /* Loop over the atoms in the i super-cluster */
+ for (int c = 0; c < gpu_ncluster_per_cell; c++)
+ {
+ c_abs = sci*gpu_ncluster_per_cell + c;
+
+ for (int i = 0; i < nbl->na_ci; i++)
+ {
+ ind_i = c_abs*nbl->na_ci + i;
+ ai = nbs->a[ind_i];
+ if (ai >= 0)
+ {
+ nri = nlist->nri;
+ nlist->jindex[nri+1] = nlist->jindex[nri];
+ nlist->iinr[nri] = ai;
+ /* With GPUs, energy groups are not supported */
+ nlist->gid[nri] = 0;
+ nlist->shift[nri] = nbl_sci->shift & NBNXN_CI_SHIFT;
+
+ bFEP_i = (gridi->fep[c_abs - gridi->cell0*gpu_ncluster_per_cell] & (1 << i));
+
+ xi = nbat->x[ind_i*nbat->xstride+XX] + shx;
+ yi = nbat->x[ind_i*nbat->xstride+YY] + shy;
+ zi = nbat->x[ind_i*nbat->xstride+ZZ] + shz;
+
+ if ((nlist->nrj + cj4_ind_end - cj4_ind_start)*nbnxn_gpu_jgroup_size*nbl->na_cj > nlist->maxnrj)
+ {
+ nlist->maxnrj = over_alloc_small((nlist->nrj + cj4_ind_end - cj4_ind_start)*nbnxn_gpu_jgroup_size*nbl->na_cj);
+ srenew(nlist->jjnr, nlist->maxnrj);
+ srenew(nlist->excl_fep, nlist->maxnrj);
+ }
+
+ for (int cj4_ind = cj4_ind_start; cj4_ind < cj4_ind_end; cj4_ind++)
+ {
+ cj4 = &nbl->cj4[cj4_ind];
+
+ for (int gcj = 0; gcj < nbnxn_gpu_jgroup_size; gcj++)
+ {
+ unsigned int fep_cj;
+
+ if ((cj4->imei[0].imask & (1U << (gcj*gpu_ncluster_per_cell + c))) == 0)
+ {
+ /* Skip this ci for this cj */
+ continue;
+ }
+
+ cjr = cj4->cj[gcj] - gridj->cell0*gpu_ncluster_per_cell;
+
+ fep_cj = gridj->fep[cjr];
+
+ if (bFEP_i || fep_cj != 0)
+ {
+ for (int j = 0; j < nbl->na_cj; j++)
+ {
+ /* Is this interaction perturbed and not excluded? */
+ ind_j = (gridj->cell0*gpu_ncluster_per_cell + cjr)*nbl->na_cj + j;
+ aj = nbs->a[ind_j];
+ if (aj >= 0 &&
+ (bFEP_i || (fep_cj & (1 << j))) &&
+ (!bDiagRemoved || ind_j >= ind_i))
+ {
+ nbnxn_excl_t *excl;
+ int excl_pair;
+ unsigned int excl_bit;
+ real dx, dy, dz;
+
+ get_nbl_exclusions_1(nbl, cj4_ind, j>>2, &excl);
+
+ excl_pair = a_mod_wj(j)*nbl->na_ci + i;
+ excl_bit = (1U << (gcj*gpu_ncluster_per_cell + c));
+
+ dx = nbat->x[ind_j*nbat->xstride+XX] - xi;
+ dy = nbat->x[ind_j*nbat->xstride+YY] - yi;
+ dz = nbat->x[ind_j*nbat->xstride+ZZ] - zi;
+
+ /* The unpruned GPU list has more than 2/3
+ * of the atom pairs beyond rlist. Using
+ * this list will cause a lot of overhead
+ * in the CPU FEP kernels, especially
+ * relative to the fast GPU kernels.
+ * So we prune the FEP list here.
+ */
+ if (dx*dx + dy*dy + dz*dz < rlist_fep2)
+ {
+ if (nlist->nrj - nlist->jindex[nri] >= max_nrj_fep)
+ {
+ fep_list_new_nri_copy(nlist);
+ nri = nlist->nri;
+ }
+
+ /* Add it to the FEP list */
+ nlist->jjnr[nlist->nrj] = aj;
+ nlist->excl_fep[nlist->nrj] = (excl->pair[excl_pair] & excl_bit) ? 1 : 0;
+ nlist->nrj++;
+ }
+
+ /* Exclude it from the normal list.
+ * Note that the charge and LJ parameters have
+ * been set to zero, but we need to avoid 0/0,
+ * as perturbed atoms can be on top of each other.
+ */
+ excl->pair[excl_pair] &= ~excl_bit;
+ }
+ }
+
+ /* Note that we could mask out this pair in imask
+ * if all i- and/or all j-particles are perturbed.
+ * But since the perturbed pairs on the CPU will
+ * take an order of magnitude more time, the GPU
+ * will finish before the CPU and there is no gain.
+ */
+ }
+ }
+ }
+
+ if (nlist->nrj > nlist->jindex[nri])
+ {
+ /* Actually add this new, non-empty, list */
+ nlist->nri++;
+ nlist->jindex[nlist->nri] = nlist->nrj;
+ }
+ }
+ }
+ }
+}
+
+/* Set all atom-pair exclusions from the topology stored in excl
+ * as masks in the pair-list for i-super-cell entry nbl_sci
+ */
+static void set_sci_top_excls(const nbnxn_search_t nbs,
+ nbnxn_pairlist_t *nbl,
+ gmx_bool diagRemoved,
+ int na_c_2log,
+ const nbnxn_sci_t *nbl_sci,
+ const t_blocka *excl)
+{
+ const int *cell;
+ int na_c;
+ int sci;
+ int cj_ind_first, cj_ind_last;
+ int cj_first, cj_last;
+ int ndirect;
+ int ai, aj, si, ge, se;
+ int found, cj_ind_0, cj_ind_1, cj_ind_m;
+ int cj_m;
+ nbnxn_excl_t *nbl_excl;
+ int inner_i, inner_e, w;
+
+ cell = nbs->cell;
+
+ na_c = nbl->na_ci;
+
+ if (nbl_sci->cj4_ind_end == nbl_sci->cj4_ind_start)
+ {
+ /* Empty list */
+ return;
+ }
+
+ sci = nbl_sci->sci;
+
+ cj_ind_first = nbl_sci->cj4_ind_start*nbnxn_gpu_jgroup_size;
+ cj_ind_last = nbl->work->cj_ind - 1;
+
+ cj_first = nbl->cj4[nbl_sci->cj4_ind_start].cj[0];
+ cj_last = nbl_cj(nbl, cj_ind_last);
+
+ /* Determine how many contiguous j-clusters we have starting
+ * from the first i-cluster. This number can be used to directly
+ * calculate j-cluster indices for excluded atoms.
+ */
+ ndirect = 0;
+ while (cj_ind_first + ndirect <= cj_ind_last &&
+ nbl_cj(nbl, cj_ind_first+ndirect) == sci*gpu_ncluster_per_cell + ndirect)
+ {
+ ndirect++;
+ }
+
+ /* Loop over the atoms in the i super-cell */
+ for (int i = 0; i < nbl->na_sc; i++)
+ {
+ ai = nbs->a[sci*nbl->na_sc+i];
+ if (ai >= 0)
+ {
+ si = (i>>na_c_2log);
+
+ /* Loop over the topology-based exclusions for this i-atom */
+ for (int eind = excl->index[ai]; eind < excl->index[ai+1]; eind++)
+ {
+ aj = excl->a[eind];
+
+ if (aj == ai)
+ {
+ /* The self exclusion are already set, save some time */
+ continue;
+ }
+
+ ge = cell[aj];
+
+ /* Without shifts we only calculate interactions j>i
+ * for one-way pair-lists.
+ */
+ if (diagRemoved && ge <= sci*nbl->na_sc + i)
+ {
+ continue;
+ }
+
+ se = ge>>na_c_2log;
+ /* Could the cluster se be in our list? */
+ if (se >= cj_first && se <= cj_last)
+ {
+ if (se < cj_first + ndirect)
+ {
+ /* We can calculate cj_ind directly from se */
+ found = cj_ind_first + se - cj_first;
+ }
+ else
+ {
+ /* Search for se using bisection */
+ found = -1;
+ cj_ind_0 = cj_ind_first + ndirect;
+ cj_ind_1 = cj_ind_last + 1;
+ while (found == -1 && cj_ind_0 < cj_ind_1)
+ {
+ cj_ind_m = (cj_ind_0 + cj_ind_1)>>1;
+
+ cj_m = nbl_cj(nbl, cj_ind_m);
+
+ if (se == cj_m)
+ {
+ found = cj_ind_m;
+ }
+ else if (se < cj_m)
+ {
+ cj_ind_1 = cj_ind_m;
+ }
+ else
+ {
+ cj_ind_0 = cj_ind_m + 1;
+ }
+ }
+ }
+
+ if (found >= 0)
+ {
+ inner_i = i - si*na_c;
+ inner_e = ge - se*na_c;
+
+ if (nbl_imask0(nbl, found) & (1U << (cj_mod_cj4(found)*gpu_ncluster_per_cell + si)))
+ {
+ w = (inner_e >> 2);
+
+ get_nbl_exclusions_1(nbl, cj_to_cj4(found), w, &nbl_excl);
+
+ nbl_excl->pair[a_mod_wj(inner_e)*nbl->na_ci+inner_i] &=
+ ~(1U << (cj_mod_cj4(found)*gpu_ncluster_per_cell + si));
+ }
+ }
+ }
+ }
+ }
+ }
+}
+
+/* Reallocate the simple ci list for at least n entries */
+static void nb_realloc_ci(nbnxn_pairlist_t *nbl, int n)
+{
+ nbl->ci_nalloc = over_alloc_small(n);
+ nbnxn_realloc_void((void **)&nbl->ci,
+ nbl->nci*sizeof(*nbl->ci),
+ nbl->ci_nalloc*sizeof(*nbl->ci),
+ nbl->alloc, nbl->free);
+}
+
+/* Reallocate the super-cell sci list for at least n entries */
+static void nb_realloc_sci(nbnxn_pairlist_t *nbl, int n)
+{
+ nbl->sci_nalloc = over_alloc_small(n);
+ nbnxn_realloc_void((void **)&nbl->sci,
+ nbl->nsci*sizeof(*nbl->sci),
+ nbl->sci_nalloc*sizeof(*nbl->sci),
+ nbl->alloc, nbl->free);
+}
+
+/* Make a new ci entry at index nbl->nci */
+static void new_ci_entry(nbnxn_pairlist_t *nbl, int ci, int shift, int flags)
+{
+ if (nbl->nci + 1 > nbl->ci_nalloc)
+ {
+ nb_realloc_ci(nbl, nbl->nci+1);
+ }
+ nbl->ci[nbl->nci].ci = ci;
+ nbl->ci[nbl->nci].shift = shift;
+ /* Store the interaction flags along with the shift */
+ nbl->ci[nbl->nci].shift |= flags;
+ nbl->ci[nbl->nci].cj_ind_start = nbl->ncj;
+ nbl->ci[nbl->nci].cj_ind_end = nbl->ncj;
+}
+
+/* Make a new sci entry at index nbl->nsci */
+static void new_sci_entry(nbnxn_pairlist_t *nbl, int sci, int shift)
+{
+ if (nbl->nsci + 1 > nbl->sci_nalloc)
+ {
+ nb_realloc_sci(nbl, nbl->nsci+1);
+ }
+ nbl->sci[nbl->nsci].sci = sci;
+ nbl->sci[nbl->nsci].shift = shift;
+ nbl->sci[nbl->nsci].cj4_ind_start = nbl->ncj4;
+ nbl->sci[nbl->nsci].cj4_ind_end = nbl->ncj4;
+}
+
+/* Sort the simple j-list cj on exclusions.
+ * Entries with exclusions will all be sorted to the beginning of the list.
+ */
+static void sort_cj_excl(nbnxn_cj_t *cj, int ncj,
+ nbnxn_list_work_t *work)
+{
+ int jnew;
+
+ if (ncj > work->cj_nalloc)
+ {
+ work->cj_nalloc = over_alloc_large(ncj);
+ srenew(work->cj, work->cj_nalloc);
+ }
+
+ /* Make a list of the j-cells involving exclusions */
+ jnew = 0;
+ for (int j = 0; j < ncj; j++)
+ {
+ if (cj[j].excl != NBNXN_INTERACTION_MASK_ALL)
+ {
+ work->cj[jnew++] = cj[j];
+ }
+ }
+ /* Check if there are exclusions at all or not just the first entry */
+ if (!((jnew == 0) ||
+ (jnew == 1 && cj[0].excl != NBNXN_INTERACTION_MASK_ALL)))
+ {
+ for (int j = 0; j < ncj; j++)
+ {
+ if (cj[j].excl == NBNXN_INTERACTION_MASK_ALL)
+ {
+ work->cj[jnew++] = cj[j];
+ }
+ }
+ for (int j = 0; j < ncj; j++)
+ {
+ cj[j] = work->cj[j];
+ }
+ }
+}
+
+/* Close this simple list i entry */
+static void close_ci_entry_simple(nbnxn_pairlist_t *nbl)
+{
+ int jlen;
+
+ /* All content of the new ci entry have already been filled correctly,
+ * we only need to increase the count here (for non empty lists).
+ */
+ jlen = nbl->ci[nbl->nci].cj_ind_end - nbl->ci[nbl->nci].cj_ind_start;
+ if (jlen > 0)
+ {
+ sort_cj_excl(nbl->cj+nbl->ci[nbl->nci].cj_ind_start, jlen, nbl->work);
+
+ /* The counts below are used for non-bonded pair/flop counts
+ * and should therefore match the available kernel setups.
+ */
+ if (!(nbl->ci[nbl->nci].shift & NBNXN_CI_DO_COUL(0)))
+ {
+ nbl->work->ncj_noq += jlen;
+ }
+ else if ((nbl->ci[nbl->nci].shift & NBNXN_CI_HALF_LJ(0)) ||
+ !(nbl->ci[nbl->nci].shift & NBNXN_CI_DO_LJ(0)))
+ {
+ nbl->work->ncj_hlj += jlen;
+ }
+
+ nbl->nci++;
+ }
+}
+
+/* Split sci entry for load balancing on the GPU.
+ * Splitting ensures we have enough lists to fully utilize the whole GPU.
+ * With progBal we generate progressively smaller lists, which improves
+ * load balancing. As we only know the current count on our own thread,
+ * we will need to estimate the current total amount of i-entries.
+ * As the lists get concatenated later, this estimate depends
+ * both on nthread and our own thread index.
+ */
+static void split_sci_entry(nbnxn_pairlist_t *nbl,
+ int nsp_target_av,
+ gmx_bool progBal, int nsp_tot_est,
+ int thread, int nthread)
+{
+ int nsp_est;
+ int nsp_max;
+ int cj4_start, cj4_end, j4len;
+ int sci;
+ int nsp, nsp_sci, nsp_cj4, nsp_cj4_e, nsp_cj4_p;
+
+ if (progBal)
+ {
+ /* Estimate the total numbers of ci's of the nblist combined
+ * over all threads using the target number of ci's.
+ */
+ nsp_est = (nsp_tot_est*thread)/nthread + nbl->nci_tot;
+
+ /* The first ci blocks should be larger, to avoid overhead.
+ * The last ci blocks should be smaller, to improve load balancing.
+ * The factor 3/2 makes the first block 3/2 times the target average
+ * and ensures that the total number of blocks end up equal to
+ * that with of equally sized blocks of size nsp_target_av.
+ */
+ nsp_max = nsp_target_av*nsp_tot_est*3/(2*(nsp_est + nsp_tot_est));
+ }
+ else
+ {
+ nsp_max = nsp_target_av;
+ }
+
+ /* Since nsp_max is a maximum/cut-off (this avoids high outliers,
+ * which lead to load imbalance), not an average, we add half the
+ * number of pairs in a cj4 block to get the average about right.
+ */
+ nsp_max += gpu_ncluster_per_cell*nbnxn_gpu_jgroup_size/2;
+
+ cj4_start = nbl->sci[nbl->nsci-1].cj4_ind_start;
+ cj4_end = nbl->sci[nbl->nsci-1].cj4_ind_end;
+ j4len = cj4_end - cj4_start;
+
+ if (j4len > 1 && j4len*gpu_ncluster_per_cell*nbnxn_gpu_jgroup_size > nsp_max)
+ {
+ /* Remove the last ci entry and process the cj4's again */
+ nbl->nsci -= 1;
+
+ sci = nbl->nsci;
+ nsp = 0;
+ nsp_sci = 0;
+ nsp_cj4_e = 0;
+ nsp_cj4 = 0;
+ for (int cj4 = cj4_start; cj4 < cj4_end; cj4++)
+ {
+ nsp_cj4_p = nsp_cj4;
+ /* Count the number of cluster pairs in this cj4 group */
+ nsp_cj4 = 0;
+ for (int p = 0; p < gpu_ncluster_per_cell*nbnxn_gpu_jgroup_size; p++)
+ {
+ nsp_cj4 += (nbl->cj4[cj4].imei[0].imask >> p) & 1;
+ }
+
+ /* Check if we should split at this cj4 to get a list of size nsp */
+ if (nsp > 0 && nsp + nsp_cj4 > nsp_max)
+ {
+ /* Split the list at cj4 */
+ nbl->sci[sci].cj4_ind_end = cj4;
+ /* Create a new sci entry */
+ sci++;
+ nbl->nsci++;
+ if (nbl->nsci+1 > nbl->sci_nalloc)
+ {
+ nb_realloc_sci(nbl, nbl->nsci+1);
+ }
+ nbl->sci[sci].sci = nbl->sci[nbl->nsci-1].sci;
+ nbl->sci[sci].shift = nbl->sci[nbl->nsci-1].shift;
+ nbl->sci[sci].cj4_ind_start = cj4;
+ nsp_sci = nsp;
+ nsp_cj4_e = nsp_cj4_p;
+ nsp = 0;
+ }
+ nsp += nsp_cj4;
+ }
+
+ /* Put the remaining cj4's in the last sci entry */
+ nbl->sci[sci].cj4_ind_end = cj4_end;
+
+ /* Possibly balance out the last two sci's
+ * by moving the last cj4 of the second last sci.
+ */
+ if (nsp_sci - nsp_cj4_e >= nsp + nsp_cj4_e)
+ {
+ nbl->sci[sci-1].cj4_ind_end--;
+ nbl->sci[sci].cj4_ind_start--;
+ }
+
+ nbl->nsci++;
+ }
+}
+
+/* Clost this super/sub list i entry */
+static void close_ci_entry_supersub(nbnxn_pairlist_t *nbl,
+ int nsp_max_av,
+ gmx_bool progBal, int nsp_tot_est,
+ int thread, int nthread)
+{
+ /* All content of the new ci entry have already been filled correctly,
+ * we only need to increase the count here (for non empty lists).
+ */
+ int j4len = nbl->sci[nbl->nsci].cj4_ind_end - nbl->sci[nbl->nsci].cj4_ind_start;
+ if (j4len > 0)
+ {
+ /* We can only have complete blocks of 4 j-entries in a list,
+ * so round the count up before closing.
+ */
+ nbl->ncj4 = (nbl->work->cj_ind + nbnxn_gpu_jgroup_size - 1)/nbnxn_gpu_jgroup_size;
+ nbl->work->cj_ind = nbl->ncj4*nbnxn_gpu_jgroup_size;
+
+ nbl->nsci++;
+
+ if (nsp_max_av > 0)
+ {
+ /* Measure the size of the new entry and potentially split it */
+ split_sci_entry(nbl, nsp_max_av, progBal, nsp_tot_est,
+ thread, nthread);
+ }
+ }
+}
+
+/* Syncs the working array before adding another grid pair to the list */
+static void sync_work(nbnxn_pairlist_t *nbl)
+{
+ if (!nbl->bSimple)
+ {
+ nbl->work->cj_ind = nbl->ncj4*nbnxn_gpu_jgroup_size;
+ nbl->work->cj4_init = nbl->ncj4;
+ }
+}
+
+/* Clears an nbnxn_pairlist_t data structure */
+static void clear_pairlist(nbnxn_pairlist_t *nbl)
+{
+ nbl->nci = 0;
+ nbl->nsci = 0;
+ nbl->ncj = 0;
+ nbl->ncj4 = 0;
+ nbl->nci_tot = 0;
+ nbl->nexcl = 1;
+
+ nbl->work->ncj_noq = 0;
+ nbl->work->ncj_hlj = 0;
+}
+
+/* Clears a group scheme pair list */
+static void clear_pairlist_fep(t_nblist *nl)
+{
+ nl->nri = 0;
+ nl->nrj = 0;
+ if (nl->jindex == NULL)
+ {
+ snew(nl->jindex, 1);
+ }
+ nl->jindex[0] = 0;
+}
+
+/* Sets a simple list i-cell bounding box, including PBC shift */
+static gmx_inline void set_icell_bb_simple(const nbnxn_bb_t *bb, int ci,
+ real shx, real shy, real shz,
+ nbnxn_bb_t *bb_ci)
+{
+ bb_ci->lower[BB_X] = bb[ci].lower[BB_X] + shx;
+ bb_ci->lower[BB_Y] = bb[ci].lower[BB_Y] + shy;
+ bb_ci->lower[BB_Z] = bb[ci].lower[BB_Z] + shz;
+ bb_ci->upper[BB_X] = bb[ci].upper[BB_X] + shx;
+ bb_ci->upper[BB_Y] = bb[ci].upper[BB_Y] + shy;
+ bb_ci->upper[BB_Z] = bb[ci].upper[BB_Z] + shz;
+}
+
+#ifdef NBNXN_BBXXXX
+/* Sets a super-cell and sub cell bounding boxes, including PBC shift */
+static void set_icell_bbxxxx_supersub(const float *bb, int ci,
+ real shx, real shy, real shz,
+ float *bb_ci)
+{
+ int ia = ci*(gpu_ncluster_per_cell >> STRIDE_PBB_2LOG)*NNBSBB_XXXX;
+ for (int m = 0; m < (gpu_ncluster_per_cell >> STRIDE_PBB_2LOG)*NNBSBB_XXXX; m += NNBSBB_XXXX)
+ {
+ for (int i = 0; i < STRIDE_PBB; i++)
+ {
+ bb_ci[m+0*STRIDE_PBB+i] = bb[ia+m+0*STRIDE_PBB+i] + shx;
+ bb_ci[m+1*STRIDE_PBB+i] = bb[ia+m+1*STRIDE_PBB+i] + shy;
+ bb_ci[m+2*STRIDE_PBB+i] = bb[ia+m+2*STRIDE_PBB+i] + shz;
+ bb_ci[m+3*STRIDE_PBB+i] = bb[ia+m+3*STRIDE_PBB+i] + shx;
+ bb_ci[m+4*STRIDE_PBB+i] = bb[ia+m+4*STRIDE_PBB+i] + shy;
+ bb_ci[m+5*STRIDE_PBB+i] = bb[ia+m+5*STRIDE_PBB+i] + shz;
+ }
+ }
+}
+#endif
+
+/* Sets a super-cell and sub cell bounding boxes, including PBC shift */
+static void set_icell_bb_supersub(const nbnxn_bb_t *bb, int ci,
+ real shx, real shy, real shz,
+ nbnxn_bb_t *bb_ci)
+{
+ for (int i = 0; i < gpu_ncluster_per_cell; i++)
+ {
+ set_icell_bb_simple(bb, ci*gpu_ncluster_per_cell+i,
+ shx, shy, shz,
+ &bb_ci[i]);
+ }
+}
+
+/* Copies PBC shifted i-cell atom coordinates x,y,z to working array */
+static void icell_set_x_simple(int ci,
+ real shx, real shy, real shz,
+ int stride, const real *x,
+ nbnxn_list_work_t *work)
+{
+ int ia = ci*NBNXN_CPU_CLUSTER_I_SIZE;
+
+ for (int i = 0; i < NBNXN_CPU_CLUSTER_I_SIZE; i++)
+ {
+ work->x_ci[i*STRIDE_XYZ+XX] = x[(ia+i)*stride+XX] + shx;
+ work->x_ci[i*STRIDE_XYZ+YY] = x[(ia+i)*stride+YY] + shy;
+ work->x_ci[i*STRIDE_XYZ+ZZ] = x[(ia+i)*stride+ZZ] + shz;
+ }
+}
+
+/* Copies PBC shifted super-cell atom coordinates x,y,z to working array */
+static void icell_set_x_supersub(int ci,
+ real shx, real shy, real shz,
+ int stride, const real *x,
+ nbnxn_list_work_t *work)
+{
+#ifndef NBNXN_SEARCH_BB_SIMD4
+
+ real * x_ci = work->x_ci;
+
+ int ia = ci*gpu_ncluster_per_cell*nbnxn_gpu_cluster_size;
+ for (int i = 0; i < gpu_ncluster_per_cell*nbnxn_gpu_cluster_size; i++)
+ {
+ x_ci[i*DIM + XX] = x[(ia+i)*stride + XX] + shx;
+ x_ci[i*DIM + YY] = x[(ia+i)*stride + YY] + shy;
+ x_ci[i*DIM + ZZ] = x[(ia+i)*stride + ZZ] + shz;
+ }
+
+#else /* !NBNXN_SEARCH_BB_SIMD4 */
+
+ real * x_ci = work->x_ci_simd;
+
+ for (int si = 0; si < gpu_ncluster_per_cell; si++)
+ {
+ for (int i = 0; i < nbnxn_gpu_cluster_size; i += GMX_SIMD4_WIDTH)
+ {
+ int io = si*nbnxn_gpu_cluster_size + i;
+ int ia = ci*gpu_ncluster_per_cell*nbnxn_gpu_cluster_size + io;
+ for (int j = 0; j < GMX_SIMD4_WIDTH; j++)
+ {
+ x_ci[io*DIM + j + XX*GMX_SIMD4_WIDTH] = x[(ia + j)*stride + XX] + shx;
+ x_ci[io*DIM + j + YY*GMX_SIMD4_WIDTH] = x[(ia + j)*stride + YY] + shy;
+ x_ci[io*DIM + j + ZZ*GMX_SIMD4_WIDTH] = x[(ia + j)*stride + ZZ] + shz;
+ }
+ }
+ }
+
+#endif /* !NBNXN_SEARCH_BB_SIMD4 */
+}
+
+static real minimum_subgrid_size_xy(const nbnxn_grid_t *grid)
+{
+ if (grid->bSimple)
+ {
+ return std::min(grid->sx, grid->sy);
+ }
+ else
+ {
+ return std::min(grid->sx/gpu_ncluster_per_cell_x,
+ grid->sy/gpu_ncluster_per_cell_y);
+ }
+}
+
+static real effective_buffer_1x1_vs_MxN(const nbnxn_grid_t *gridi,
+ const nbnxn_grid_t *gridj)
+{
+ const real eff_1x1_buffer_fac_overest = 0.1;
+
+ /* Determine an atom-pair list cut-off buffer size for atom pairs,
+ * to be added to rlist (including buffer) used for MxN.
+ * This is for converting an MxN list to a 1x1 list. This means we can't
+ * use the normal buffer estimate, as we have an MxN list in which
+ * some atom pairs beyond rlist are missing. We want to capture
+ * the beneficial effect of buffering by extra pairs just outside rlist,
+ * while removing the useless pairs that are further away from rlist.
+ * (Also the buffer could have been set manually not using the estimate.)
+ * This buffer size is an overestimate.
+ * We add 10% of the smallest grid sub-cell dimensions.
+ * Note that the z-size differs per cell and we don't use this,
+ * so we overestimate.
+ * With PME, the 10% value gives a buffer that is somewhat larger
+ * than the effective buffer with a tolerance of 0.005 kJ/mol/ps.
+ * Smaller tolerances or using RF lead to a smaller effective buffer,
+ * so 10% gives a safe overestimate.
+ */
+ return eff_1x1_buffer_fac_overest*(minimum_subgrid_size_xy(gridi) +
+ minimum_subgrid_size_xy(gridj));
+}
+
+/* Clusters at the cut-off only increase rlist by 60% of their size */
+static real nbnxn_rlist_inc_outside_fac = 0.6;
+
+/* Due to the cluster size the effective pair-list is longer than
+ * that of a simple atom pair-list. This function gives the extra distance.
+ */
+real nbnxn_get_rlist_effective_inc(int cluster_size_j, real atom_density)
+{
+ int cluster_size_i;
+ real vol_inc_i, vol_inc_j;
+
+ /* We should get this from the setup, but currently it's the same for
+ * all setups, including GPUs.
+ */
+ cluster_size_i = NBNXN_CPU_CLUSTER_I_SIZE;
+
+ vol_inc_i = (cluster_size_i - 1)/atom_density;
+ vol_inc_j = (cluster_size_j - 1)/atom_density;
+
+ return nbnxn_rlist_inc_outside_fac*std::cbrt(vol_inc_i + vol_inc_j);
+}
+
+/* Estimates the interaction volume^2 for non-local interactions */
+static real nonlocal_vol2(const struct gmx_domdec_zones_t *zones, rvec ls, real r)
+{
+ real cl, ca, za;
+ real vold_est;
+ real vol2_est_tot;
+
+ vol2_est_tot = 0;
+
+ /* Here we simply add up the volumes of 1, 2 or 3 1D decomposition
+ * not home interaction volume^2. As these volumes are not additive,
+ * this is an overestimate, but it would only be significant in the limit
+ * of small cells, where we anyhow need to split the lists into
+ * as small parts as possible.
+ */
+
+ for (int z = 0; z < zones->n; z++)
+ {
+ if (zones->shift[z][XX] + zones->shift[z][YY] + zones->shift[z][ZZ] == 1)
+ {
+ cl = 0;
+ ca = 1;
+ za = 1;
+ for (int d = 0; d < DIM; d++)
+ {
+ if (zones->shift[z][d] == 0)
+ {
+ cl += 0.5*ls[d];
+ ca *= ls[d];
+ za *= zones->size[z].x1[d] - zones->size[z].x0[d];
+ }
+ }
+
+ /* 4 octants of a sphere */
+ vold_est = 0.25*M_PI*r*r*r*r;
+ /* 4 quarter pie slices on the edges */
+ vold_est += 4*cl*M_PI/6.0*r*r*r;
+ /* One rectangular volume on a face */
+ vold_est += ca*0.5*r*r;
+
+ vol2_est_tot += vold_est*za;
+ }
+ }
+
+ return vol2_est_tot;
+}
+
+/* Estimates the average size of a full j-list for super/sub setup */
+static void get_nsubpair_target(const nbnxn_search_t nbs,
+ int iloc,
+ real rlist,
+ int min_ci_balanced,
+ int *nsubpair_target,
+ int *nsubpair_tot_est)
+{
+ /* The target value of 36 seems to be the optimum for Kepler.
+ * Maxwell is less sensitive to the exact value.
+ */
+ const int nsubpair_target_min = 36;
+ const nbnxn_grid_t *grid;
+ rvec ls;
+ real xy_diag2, r_eff_sup, vol_est, nsp_est, nsp_est_nl;
+
+ grid = &nbs->grid[0];
+
+ if (min_ci_balanced <= 0 || grid->nc >= min_ci_balanced || grid->nc == 0)
+ {
+ /* We don't need to balance the list sizes */
+ *nsubpair_target = 0;
+ *nsubpair_tot_est = 0;
+
+ return;
+ }
+
+ ls[XX] = (grid->c1[XX] - grid->c0[XX])/(grid->ncx*gpu_ncluster_per_cell_x);
+ ls[YY] = (grid->c1[YY] - grid->c0[YY])/(grid->ncy*gpu_ncluster_per_cell_y);
+ ls[ZZ] = grid->na_c/(grid->atom_density*ls[XX]*ls[YY]);
+
+ /* The average squared length of the diagonal of a sub cell */
+ xy_diag2 = ls[XX]*ls[XX] + ls[YY]*ls[YY] + ls[ZZ]*ls[ZZ];
+
+ /* The formulas below are a heuristic estimate of the average nsj per si*/
+ r_eff_sup = rlist + nbnxn_rlist_inc_outside_fac*gmx::square((grid->na_c - 1.0)/grid->na_c)*std::sqrt(xy_diag2/3);
+
+ if (!nbs->DomDec || nbs->zones->n == 1)
+ {
+ nsp_est_nl = 0;
+ }
+ else
+ {
+ nsp_est_nl =
+ gmx::square(grid->atom_density/grid->na_c)*
+ nonlocal_vol2(nbs->zones, ls, r_eff_sup);
+ }
+
+ if (LOCAL_I(iloc))
+ {
+ /* Sub-cell interacts with itself */
+ vol_est = ls[XX]*ls[YY]*ls[ZZ];
+ /* 6/2 rectangular volume on the faces */
+ vol_est += (ls[XX]*ls[YY] + ls[XX]*ls[ZZ] + ls[YY]*ls[ZZ])*r_eff_sup;
+ /* 12/2 quarter pie slices on the edges */
+ vol_est += 2*(ls[XX] + ls[YY] + ls[ZZ])*0.25*M_PI*gmx::square(r_eff_sup);
+ /* 4 octants of a sphere */
+ vol_est += 0.5*4.0/3.0*M_PI*gmx::power3(r_eff_sup);
+
+ /* Estimate the number of cluster pairs as the local number of
+ * clusters times the volume they interact with times the density.
+ */
+ nsp_est = grid->nsubc_tot*vol_est*grid->atom_density/grid->na_c;
+
+ /* Subtract the non-local pair count */
+ nsp_est -= nsp_est_nl;
+
+ /* For small cut-offs nsp_est will be an underesimate.
+ * With DD nsp_est_nl is an overestimate so nsp_est can get negative.
+ * So to avoid too small or negative nsp_est we set a minimum of
+ * all cells interacting with all 3^3 direct neighbors (3^3-1)/2+1=14.
+ * This might be a slight overestimate for small non-periodic groups of
+ * atoms as will occur for a local domain with DD, but for small
+ * groups of atoms we'll anyhow be limited by nsubpair_target_min,
+ * so this overestimation will not matter.
+ */
+ nsp_est = std::max(nsp_est, grid->nsubc_tot*static_cast<real>(14));
+
+ if (debug)
+ {
+ fprintf(debug, "nsp_est local %5.1f non-local %5.1f\n",
+ nsp_est, nsp_est_nl);
+ }
+ }
+ else
+ {
+ nsp_est = nsp_est_nl;
+ }
+
+ /* Thus the (average) maximum j-list size should be as follows.
+ * Since there is overhead, we shouldn't make the lists too small
+ * (and we can't chop up j-groups) so we use a minimum target size of 36.
+ */
+ *nsubpair_target = std::max(nsubpair_target_min,
+ static_cast<int>(nsp_est/min_ci_balanced + 0.5));
+ *nsubpair_tot_est = static_cast<int>(nsp_est);
+
+ if (debug)
+ {
+ fprintf(debug, "nbl nsp estimate %.1f, nsubpair_target %d\n",
+ nsp_est, *nsubpair_target);
+ }
+}
+
+/* Debug list print function */
+static void print_nblist_ci_cj(FILE *fp, const nbnxn_pairlist_t *nbl)
+{
+ for (int i = 0; i < nbl->nci; i++)
+ {
+ fprintf(fp, "ci %4d shift %2d ncj %3d\n",
+ nbl->ci[i].ci, nbl->ci[i].shift,
+ nbl->ci[i].cj_ind_end - nbl->ci[i].cj_ind_start);
+
+ for (int j = nbl->ci[i].cj_ind_start; j < nbl->ci[i].cj_ind_end; j++)
+ {
+ fprintf(fp, " cj %5d imask %x\n",
+ nbl->cj[j].cj,
+ nbl->cj[j].excl);
+ }
+ }
+}
+
+/* Debug list print function */
+static void print_nblist_sci_cj(FILE *fp, const nbnxn_pairlist_t *nbl)
+{
+ for (int i = 0; i < nbl->nsci; i++)
+ {
+ fprintf(fp, "ci %4d shift %2d ncj4 %2d\n",
+ nbl->sci[i].sci, nbl->sci[i].shift,
+ nbl->sci[i].cj4_ind_end - nbl->sci[i].cj4_ind_start);
+
+ int ncp = 0;
+ for (int j4 = nbl->sci[i].cj4_ind_start; j4 < nbl->sci[i].cj4_ind_end; j4++)
+ {
+ for (int j = 0; j < nbnxn_gpu_jgroup_size; j++)
+ {
+ fprintf(fp, " sj %5d imask %x\n",
+ nbl->cj4[j4].cj[j],
+ nbl->cj4[j4].imei[0].imask);
+ for (int si = 0; si < gpu_ncluster_per_cell; si++)
+ {
+ if (nbl->cj4[j4].imei[0].imask & (1U << (j*gpu_ncluster_per_cell + si)))
+ {
+ ncp++;
+ }
+ }
+ }
+ }
+ fprintf(fp, "ci %4d shift %2d ncj4 %2d ncp %3d\n",
+ nbl->sci[i].sci, nbl->sci[i].shift,
+ nbl->sci[i].cj4_ind_end - nbl->sci[i].cj4_ind_start,
+ ncp);
+ }
+}
+
+/* Combine pair lists *nbl generated on multiple threads nblc */
+static void combine_nblists(int nnbl, nbnxn_pairlist_t **nbl,
+ nbnxn_pairlist_t *nblc)
+{
+ int nsci, ncj4, nexcl;
+
+ if (nblc->bSimple)
+ {
+ gmx_incons("combine_nblists does not support simple lists");
+ }
+
+ nsci = nblc->nsci;
+ ncj4 = nblc->ncj4;
+ nexcl = nblc->nexcl;
+ for (int i = 0; i < nnbl; i++)
+ {
+ nsci += nbl[i]->nsci;
+ ncj4 += nbl[i]->ncj4;
+ nexcl += nbl[i]->nexcl;
+ }
+
+ if (nsci > nblc->sci_nalloc)
+ {
+ nb_realloc_sci(nblc, nsci);
+ }
+ if (ncj4 > nblc->cj4_nalloc)
+ {
+ nblc->cj4_nalloc = over_alloc_small(ncj4);
+ nbnxn_realloc_void((void **)&nblc->cj4,
+ nblc->ncj4*sizeof(*nblc->cj4),
+ nblc->cj4_nalloc*sizeof(*nblc->cj4),
+ nblc->alloc, nblc->free);
+ }
+ if (nexcl > nblc->excl_nalloc)
+ {
+ nblc->excl_nalloc = over_alloc_small(nexcl);
+ nbnxn_realloc_void((void **)&nblc->excl,
+ nblc->nexcl*sizeof(*nblc->excl),
+ nblc->excl_nalloc*sizeof(*nblc->excl),
+ nblc->alloc, nblc->free);
+ }
+
+ /* Each thread should copy its own data to the combined arrays,
+ * as otherwise data will go back and forth between different caches.
+ */
+#if GMX_OPENMP && !(defined __clang_analyzer__)
+ // cppcheck-suppress unreadVariable
+ int nthreads = gmx_omp_nthreads_get(emntPairsearch);
+#endif
+
+#pragma omp parallel for num_threads(nthreads) schedule(static)
+ for (int n = 0; n < nnbl; n++)
+ {
+ try
+ {
+ int sci_offset;
+ int cj4_offset;
+ int excl_offset;
+ const nbnxn_pairlist_t *nbli;
+
+ /* Determine the offset in the combined data for our thread */
+ sci_offset = nblc->nsci;
+ cj4_offset = nblc->ncj4;
+ excl_offset = nblc->nexcl;
+
+ for (int i = 0; i < n; i++)
+ {
+ sci_offset += nbl[i]->nsci;
+ cj4_offset += nbl[i]->ncj4;
+ excl_offset += nbl[i]->nexcl;
+ }
+
+ nbli = nbl[n];
+
+ for (int i = 0; i < nbli->nsci; i++)
+ {
+ nblc->sci[sci_offset+i] = nbli->sci[i];
+ nblc->sci[sci_offset+i].cj4_ind_start += cj4_offset;
+ nblc->sci[sci_offset+i].cj4_ind_end += cj4_offset;
+ }
+
+ for (int j4 = 0; j4 < nbli->ncj4; j4++)
+ {
+ nblc->cj4[cj4_offset+j4] = nbli->cj4[j4];
+ nblc->cj4[cj4_offset+j4].imei[0].excl_ind += excl_offset;
+ nblc->cj4[cj4_offset+j4].imei[1].excl_ind += excl_offset;
+ }
+
+ for (int j4 = 0; j4 < nbli->nexcl; j4++)
+ {
+ nblc->excl[excl_offset+j4] = nbli->excl[j4];
+ }
+ }
+ GMX_CATCH_ALL_AND_EXIT_WITH_FATAL_ERROR;
+ }
+
+ for (int n = 0; n < nnbl; n++)
+ {
+ nblc->nsci += nbl[n]->nsci;
+ nblc->ncj4 += nbl[n]->ncj4;
+ nblc->nci_tot += nbl[n]->nci_tot;
+ nblc->nexcl += nbl[n]->nexcl;
+ }
+}
+
+static void balance_fep_lists(const nbnxn_search_t nbs,
+ nbnxn_pairlist_set_t *nbl_lists)
+{
+ int nnbl;
+ int nri_tot, nrj_tot, nrj_target;
+ int th_dest;
+ t_nblist *nbld;
+
+ nnbl = nbl_lists->nnbl;
+
+ if (nnbl == 1)
+ {
+ /* Nothing to balance */
+ return;
+ }
+
+ /* Count the total i-lists and pairs */
+ nri_tot = 0;
+ nrj_tot = 0;
+ for (int th = 0; th < nnbl; th++)
+ {
+ nri_tot += nbl_lists->nbl_fep[th]->nri;
+ nrj_tot += nbl_lists->nbl_fep[th]->nrj;
+ }
+
+ nrj_target = (nrj_tot + nnbl - 1)/nnbl;
+
+ assert(gmx_omp_nthreads_get(emntNonbonded) == nnbl);
+
+#pragma omp parallel for schedule(static) num_threads(nnbl)
+ for (int th = 0; th < nnbl; th++)
+ {
+ try
+ {
+ t_nblist *nbl;
+
+ nbl = nbs->work[th].nbl_fep;
+
+ /* Note that here we allocate for the total size, instead of
+ * a per-thread esimate (which is hard to obtain).
+ */
+ if (nri_tot > nbl->maxnri)
+ {
+ nbl->maxnri = over_alloc_large(nri_tot);
+ reallocate_nblist(nbl);
+ }
+ if (nri_tot > nbl->maxnri || nrj_tot > nbl->maxnrj)
+ {
+ nbl->maxnrj = over_alloc_small(nrj_tot);
+ srenew(nbl->jjnr, nbl->maxnrj);
+ srenew(nbl->excl_fep, nbl->maxnrj);
+ }
+
+ clear_pairlist_fep(nbl);
+ }
+ GMX_CATCH_ALL_AND_EXIT_WITH_FATAL_ERROR;
+ }
+
+ /* Loop over the source lists and assign and copy i-entries */
+ th_dest = 0;
+ nbld = nbs->work[th_dest].nbl_fep;
+ for (int th = 0; th < nnbl; th++)
+ {
+ t_nblist *nbls;
+
+ nbls = nbl_lists->nbl_fep[th];
+
+ for (int i = 0; i < nbls->nri; i++)
+ {
+ int nrj;
+
+ /* The number of pairs in this i-entry */
+ nrj = nbls->jindex[i+1] - nbls->jindex[i];
+
+ /* Decide if list th_dest is too large and we should procede
+ * to the next destination list.
+ */
+ if (th_dest+1 < nnbl && nbld->nrj > 0 &&
+ nbld->nrj + nrj - nrj_target > nrj_target - nbld->nrj)
+ {
+ th_dest++;
+ nbld = nbs->work[th_dest].nbl_fep;
+ }
+
+ nbld->iinr[nbld->nri] = nbls->iinr[i];
+ nbld->gid[nbld->nri] = nbls->gid[i];
+ nbld->shift[nbld->nri] = nbls->shift[i];
+
+ for (int j = nbls->jindex[i]; j < nbls->jindex[i+1]; j++)
+ {
+ nbld->jjnr[nbld->nrj] = nbls->jjnr[j];
+ nbld->excl_fep[nbld->nrj] = nbls->excl_fep[j];
+ nbld->nrj++;
+ }
+ nbld->nri++;
+ nbld->jindex[nbld->nri] = nbld->nrj;
+ }
+ }
+
+ /* Swap the list pointers */
+ for (int th = 0; th < nnbl; th++)
+ {
+ t_nblist *nbl_tmp;
+
+ nbl_tmp = nbl_lists->nbl_fep[th];
+ nbl_lists->nbl_fep[th] = nbs->work[th].nbl_fep;
+ nbs->work[th].nbl_fep = nbl_tmp;
+
+ if (debug)
+ {
+ fprintf(debug, "nbl_fep[%d] nri %4d nrj %4d\n",
+ th,
+ nbl_lists->nbl_fep[th]->nri,
+ nbl_lists->nbl_fep[th]->nrj);
+ }
+ }
+}
+
+/* Returns the next ci to be processes by our thread */
+static gmx_bool next_ci(const nbnxn_grid_t *grid,
+ int conv,
+ int nth, int ci_block,
+ int *ci_x, int *ci_y,
+ int *ci_b, int *ci)
+{
+ (*ci_b)++;
+ (*ci)++;
+
+ if (*ci_b == ci_block)
+ {
+ /* Jump to the next block assigned to this task */
+ *ci += (nth - 1)*ci_block;
+ *ci_b = 0;
+ }
+
+ if (*ci >= grid->nc*conv)
+ {
+ return FALSE;
+ }
+
+ while (*ci >= grid->cxy_ind[*ci_x*grid->ncy + *ci_y + 1]*conv)
+ {
+ *ci_y += 1;
+ if (*ci_y == grid->ncy)
+ {
+ *ci_x += 1;
+ *ci_y = 0;
+ }
+ }
+
+ return TRUE;
+}
+
+/* Returns the distance^2 for which we put cell pairs in the list
+ * without checking atom pair distances. This is usually < rlist^2.
+ */
+static float boundingbox_only_distance2(const nbnxn_grid_t *gridi,
+ const nbnxn_grid_t *gridj,
+ real rlist,
+ gmx_bool simple)
+{
+ /* If the distance between two sub-cell bounding boxes is less
+ * than this distance, do not check the distance between
+ * all particle pairs in the sub-cell, since then it is likely
+ * that the box pair has atom pairs within the cut-off.
+ * We use the nblist cut-off minus 0.5 times the average x/y diagonal
+ * spacing of the sub-cells. Around 40% of the checked pairs are pruned.
+ * Using more than 0.5 gains at most 0.5%.
+ * If forces are calculated more than twice, the performance gain
+ * in the force calculation outweighs the cost of checking.
+ * Note that with subcell lists, the atom-pair distance check
+ * is only performed when only 1 out of 8 sub-cells in within range,
+ * this is because the GPU is much faster than the cpu.
+ */
+ real bbx, bby;
+ real rbb2;
+
+ bbx = 0.5*(gridi->sx + gridj->sx);
+ bby = 0.5*(gridi->sy + gridj->sy);
+ if (!simple)
+ {
+ bbx /= gpu_ncluster_per_cell_x;
+ bby /= gpu_ncluster_per_cell_y;
+ }
+
+ rbb2 = std::max(0.0, rlist - 0.5*std::sqrt(bbx*bbx + bby*bby));
+ rbb2 = rbb2 * rbb2;
+
+#if !GMX_DOUBLE
+ return rbb2;
+#else
+ return (float)((1+GMX_FLOAT_EPS)*rbb2);
+#endif
+}
+
+static int get_ci_block_size(const nbnxn_grid_t *gridi,
+ gmx_bool bDomDec, int nth)
+{
+ const int ci_block_enum = 5;
+ const int ci_block_denom = 11;
+ const int ci_block_min_atoms = 16;
+ int ci_block;
+
+ /* Here we decide how to distribute the blocks over the threads.
+ * We use prime numbers to try to avoid that the grid size becomes
+ * a multiple of the number of threads, which would lead to some
+ * threads getting "inner" pairs and others getting boundary pairs,
+ * which in turns will lead to load imbalance between threads.
+ * Set the block size as 5/11/ntask times the average number of cells
+ * in a y,z slab. This should ensure a quite uniform distribution
+ * of the grid parts of the different thread along all three grid
+ * zone boundaries with 3D domain decomposition. At the same time
+ * the blocks will not become too small.
+ */
+ ci_block = (gridi->nc*ci_block_enum)/(ci_block_denom*gridi->ncx*nth);
+
+ /* Ensure the blocks are not too small: avoids cache invalidation */
+ if (ci_block*gridi->na_sc < ci_block_min_atoms)
+ {
+ ci_block = (ci_block_min_atoms + gridi->na_sc - 1)/gridi->na_sc;
+ }
+
+ /* Without domain decomposition
+ * or with less than 3 blocks per task, divide in nth blocks.
+ */
+ if (!bDomDec || nth*3*ci_block > gridi->nc)
+ {
+ ci_block = (gridi->nc + nth - 1)/nth;
+ }
+
+ if (ci_block > 1 && (nth - 1)*ci_block >= gridi->nc)
+ {
+ /* Some threads have no work. Although reducing the block size
+ * does not decrease the block count on the first few threads,
+ * with GPUs better mixing of "upper" cells that have more empty
+ * clusters results in a somewhat lower max load over all threads.
+ * Without GPUs the regime of so few atoms per thread is less
+ * performance relevant, but with 8-wide SIMD the same reasoning
+ * applies, since the pair list uses 4 i-atom "sub-clusters".
+ */
+ ci_block--;
+ }
+
+ return ci_block;
+}
+
+/* Generates the part of pair-list nbl assigned to our thread */
+static void nbnxn_make_pairlist_part(const nbnxn_search_t nbs,
+ const nbnxn_grid_t *gridi,
+ const nbnxn_grid_t *gridj,
+ nbnxn_search_work_t *work,
+ const nbnxn_atomdata_t *nbat,
+ const t_blocka *excl,
+ real rlist,
+ int nb_kernel_type,
+ int ci_block,
+ gmx_bool bFBufferFlag,
+ int nsubpair_max,
+ gmx_bool progBal,
+ int nsubpair_tot_est,
+ int th, int nth,
+ nbnxn_pairlist_t *nbl,
+ t_nblist *nbl_fep)
+{
+ int na_cj_2log;
+ matrix box;
+ real rl2, rl_fep2 = 0;
+ float rbb2;
+ int ci_b, ci, ci_x, ci_y, ci_xy, cj;
+ ivec shp;
+ int shift;
+ real shx, shy, shz;
+ int conv_i, cell0_i;
+ const nbnxn_bb_t *bb_i = NULL;
+#ifdef NBNXN_BBXXXX
+ const float *pbb_i = NULL;
+#endif
+ const float *bbcz_i, *bbcz_j;
+ const int *flags_i;
+ real bx0, bx1, by0, by1, bz0, bz1;
+ real bz1_frac;
+ real d2cx, d2z, d2z_cx, d2z_cy, d2zx, d2zxy, d2xy;
+ int cxf, cxl, cyf, cyf_x, cyl;
+ int c0, c1, cs, cf, cl;
+ int ndistc;
+ int ncpcheck;
+ int gridi_flag_shift = 0, gridj_flag_shift = 0;
+ gmx_bitmask_t *gridj_flag = NULL;
+ int ncj_old_i, ncj_old_j;
+
+ nbs_cycle_start(&work->cc[enbsCCsearch]);
+
+ if (gridj->bSimple != nbl->bSimple)
+ {
+ gmx_incons("Grid incompatible with pair-list");
+ }
+
+ sync_work(nbl);
+ nbl->na_sc = gridj->na_sc;
+ nbl->na_ci = gridj->na_c;
+ nbl->na_cj = nbnxn_kernel_to_cluster_j_size(nb_kernel_type);
+ na_cj_2log = get_2log(nbl->na_cj);
+
+ nbl->rlist = rlist;
+
+ if (bFBufferFlag)
+ {
+ /* Determine conversion of clusters to flag blocks */
+ gridi_flag_shift = 0;
+ while ((nbl->na_ci<<gridi_flag_shift) < NBNXN_BUFFERFLAG_SIZE)
+ {
+ gridi_flag_shift++;
+ }
+ gridj_flag_shift = 0;
+ while ((nbl->na_cj<<gridj_flag_shift) < NBNXN_BUFFERFLAG_SIZE)
+ {
+ gridj_flag_shift++;
+ }
+
+ gridj_flag = work->buffer_flags.flag;
+ }
+
+ copy_mat(nbs->box, box);
+
+ rl2 = nbl->rlist*nbl->rlist;
+
+ if (nbs->bFEP && !nbl->bSimple)
+ {
+ /* Determine an atom-pair list cut-off distance for FEP atom pairs.
+ * We should not simply use rlist, since then we would not have
+ * the small, effective buffering of the NxN lists.
+ * The buffer is on overestimate, but the resulting cost for pairs
+ * beyond rlist is neglible compared to the FEP pairs within rlist.
+ */
+ rl_fep2 = nbl->rlist + effective_buffer_1x1_vs_MxN(gridi, gridj);
+
+ if (debug)
+ {
+ fprintf(debug, "nbl_fep atom-pair rlist %f\n", rl_fep2);
+ }
+ rl_fep2 = rl_fep2*rl_fep2;
+ }
+
+ rbb2 = boundingbox_only_distance2(gridi, gridj, nbl->rlist, nbl->bSimple);
+
+ if (debug)
+ {
+ fprintf(debug, "nbl bounding box only distance %f\n", std::sqrt(rbb2));
+ }
+
+ /* Set the shift range */
+ for (int d = 0; d < DIM; d++)
+ {
+ /* Check if we need periodicity shifts.
+ * Without PBC or with domain decomposition we don't need them.
+ */
+ if (d >= ePBC2npbcdim(nbs->ePBC) || nbs->dd_dim[d])
+ {
+ shp[d] = 0;
+ }
+ else
+ {
+ if (d == XX &&
+ box[XX][XX] - fabs(box[YY][XX]) - fabs(box[ZZ][XX]) < std::sqrt(rl2))
+ {
+ shp[d] = 2;
+ }
+ else
+ {
+ shp[d] = 1;
+ }
+ }
+ }
+
+ if (nbl->bSimple && !gridi->bSimple)
+ {
+ conv_i = gridi->na_sc/gridj->na_sc;
+ bb_i = gridi->bb_simple;
+ bbcz_i = gridi->bbcz_simple;
+ flags_i = gridi->flags_simple;
+ }
+ else
+ {
+ conv_i = 1;
+#ifdef NBNXN_BBXXXX
+ if (gridi->bSimple)
+ {
+ bb_i = gridi->bb;
+ }
+ else
+ {
+ pbb_i = gridi->pbb;
+ }
+#else
+ /* We use the normal bounding box format for both grid types */
+ bb_i = gridi->bb;
+#endif
+ bbcz_i = gridi->bbcz;
+ flags_i = gridi->flags;
+ }
+ cell0_i = gridi->cell0*conv_i;
+
+ bbcz_j = gridj->bbcz;
+
+ if (conv_i != 1)
+ {
+ /* Blocks of the conversion factor - 1 give a large repeat count
+ * combined with a small block size. This should result in good
+ * load balancing for both small and large domains.
+ */
+ ci_block = conv_i - 1;
+ }
+ if (debug)
+ {
+ fprintf(debug, "nbl nc_i %d col.av. %.1f ci_block %d\n",
+ gridi->nc, gridi->nc/(double)(gridi->ncx*gridi->ncy), ci_block);
+ }
+
+ ndistc = 0;
+ ncpcheck = 0;
+
+ /* Initially ci_b and ci to 1 before where we want them to start,
+ * as they will both be incremented in next_ci.
+ */
+ ci_b = -1;
+ ci = th*ci_block - 1;
+ ci_x = 0;
+ ci_y = 0;
+ while (next_ci(gridi, conv_i, nth, ci_block, &ci_x, &ci_y, &ci_b, &ci))
+ {
+ if (nbl->bSimple && flags_i[ci] == 0)
+ {
+ continue;
+ }
+
+ ncj_old_i = nbl->ncj;
+
+ d2cx = 0;
+ if (gridj != gridi && shp[XX] == 0)
+ {
+ if (nbl->bSimple)
+ {
+ bx1 = bb_i[ci].upper[BB_X];
+ }
+ else
+ {
+ bx1 = gridi->c0[XX] + (ci_x+1)*gridi->sx;
+ }
+ if (bx1 < gridj->c0[XX])
+ {
+ d2cx = gmx::square(gridj->c0[XX] - bx1);
+
+ if (d2cx >= rl2)
+ {
+ continue;
+ }
+ }
+ }
+
+ ci_xy = ci_x*gridi->ncy + ci_y;
+
+ /* Loop over shift vectors in three dimensions */
+ for (int tz = -shp[ZZ]; tz <= shp[ZZ]; tz++)
+ {
+ shz = tz*box[ZZ][ZZ];
+
+ bz0 = bbcz_i[ci*NNBSBB_D ] + shz;
+ bz1 = bbcz_i[ci*NNBSBB_D+1] + shz;
+
+ if (tz == 0)
+ {
+ d2z = 0;
+ }
+ else if (tz < 0)
+ {
+ d2z = gmx::square(bz1);
+ }
+ else
+ {
+ d2z = gmx::square(bz0 - box[ZZ][ZZ]);
+ }
+
+ d2z_cx = d2z + d2cx;
+
+ if (d2z_cx >= rl2)
+ {
+ continue;
+ }
+
+ bz1_frac = bz1/(gridi->cxy_ind[ci_xy+1] - gridi->cxy_ind[ci_xy]);
+ if (bz1_frac < 0)
+ {
+ bz1_frac = 0;
+ }
+ /* The check with bz1_frac close to or larger than 1 comes later */
+
+ for (int ty = -shp[YY]; ty <= shp[YY]; ty++)
+ {
+ shy = ty*box[YY][YY] + tz*box[ZZ][YY];
+
+ if (nbl->bSimple)
+ {
+ by0 = bb_i[ci].lower[BB_Y] + shy;
+ by1 = bb_i[ci].upper[BB_Y] + shy;
+ }
+ else
+ {
+ by0 = gridi->c0[YY] + (ci_y )*gridi->sy + shy;
+ by1 = gridi->c0[YY] + (ci_y+1)*gridi->sy + shy;
+ }
+
+ get_cell_range(by0, by1,
+ gridj->ncy, gridj->c0[YY], gridj->sy, gridj->inv_sy,
+ d2z_cx, rl2,
+ &cyf, &cyl);
+
+ if (cyf > cyl)
+ {
+ continue;
+ }
+
+ d2z_cy = d2z;
+ if (by1 < gridj->c0[YY])
+ {
+ d2z_cy += gmx::square(gridj->c0[YY] - by1);
+ }
+ else if (by0 > gridj->c1[YY])
+ {
+ d2z_cy += gmx::square(by0 - gridj->c1[YY]);
+ }
+
+ for (int tx = -shp[XX]; tx <= shp[XX]; tx++)
+ {
+ shift = XYZ2IS(tx, ty, tz);
+
+#ifdef NBNXN_SHIFT_BACKWARD
+ if (gridi == gridj && shift > CENTRAL)
+ {
+ continue;
+ }
+#endif
+
+ shx = tx*box[XX][XX] + ty*box[YY][XX] + tz*box[ZZ][XX];
+
+ if (nbl->bSimple)
+ {
+ bx0 = bb_i[ci].lower[BB_X] + shx;
+ bx1 = bb_i[ci].upper[BB_X] + shx;
+ }
+ else
+ {
+ bx0 = gridi->c0[XX] + (ci_x )*gridi->sx + shx;
+ bx1 = gridi->c0[XX] + (ci_x+1)*gridi->sx + shx;
+ }
+
+ get_cell_range(bx0, bx1,
+ gridj->ncx, gridj->c0[XX], gridj->sx, gridj->inv_sx,
+ d2z_cy, rl2,
+ &cxf, &cxl);
+
+ if (cxf > cxl)
+ {
+ continue;
+ }
+
+ if (nbl->bSimple)
+ {
+ new_ci_entry(nbl, cell0_i+ci, shift, flags_i[ci]);
+ }
+ else
+ {
+ new_sci_entry(nbl, cell0_i+ci, shift);
+ }
+
+#ifndef NBNXN_SHIFT_BACKWARD
+ if (cxf < ci_x)
+#else
+ if (shift == CENTRAL && gridi == gridj &&
+ cxf < ci_x)
+#endif
+ {
+ /* Leave the pairs with i > j.
+ * x is the major index, so skip half of it.
+ */
+ cxf = ci_x;
+ }
+
+ if (nbl->bSimple)
+ {
+ set_icell_bb_simple(bb_i, ci, shx, shy, shz,
+ nbl->work->bb_ci);
+ }
+ else
+ {
+#ifdef NBNXN_BBXXXX
+ set_icell_bbxxxx_supersub(pbb_i, ci, shx, shy, shz,
+ nbl->work->pbb_ci);
+#else
+ set_icell_bb_supersub(bb_i, ci, shx, shy, shz,
+ nbl->work->bb_ci);
+#endif
+ }
+
+ nbs->icell_set_x(cell0_i+ci, shx, shy, shz,
+ nbat->xstride, nbat->x,
+ nbl->work);
+
+ for (int cx = cxf; cx <= cxl; cx++)
+ {
+ d2zx = d2z;
+ if (gridj->c0[XX] + cx*gridj->sx > bx1)
+ {
+ d2zx += gmx::square(gridj->c0[XX] + cx*gridj->sx - bx1);
+ }
+ else if (gridj->c0[XX] + (cx+1)*gridj->sx < bx0)
+ {
+ d2zx += gmx::square(gridj->c0[XX] + (cx+1)*gridj->sx - bx0);
+ }
+
+#ifndef NBNXN_SHIFT_BACKWARD
+ if (gridi == gridj &&
+ cx == 0 && cyf < ci_y)
+#else
+ if (gridi == gridj &&
+ cx == 0 && shift == CENTRAL && cyf < ci_y)
+#endif
+ {
+ /* Leave the pairs with i > j.
+ * Skip half of y when i and j have the same x.
+ */
+ cyf_x = ci_y;
+ }
+ else
+ {
+ cyf_x = cyf;
+ }
+
+ for (int cy = cyf_x; cy <= cyl; cy++)
+ {
+ c0 = gridj->cxy_ind[cx*gridj->ncy+cy];
+ c1 = gridj->cxy_ind[cx*gridj->ncy+cy+1];
+#ifdef NBNXN_SHIFT_BACKWARD
+ if (gridi == gridj &&
+ shift == CENTRAL && c0 < ci)
+ {
+ c0 = ci;
+ }
+#endif
+
+ d2zxy = d2zx;
+ if (gridj->c0[YY] + cy*gridj->sy > by1)
+ {
+ d2zxy += gmx::square(gridj->c0[YY] + cy*gridj->sy - by1);
+ }
+ else if (gridj->c0[YY] + (cy+1)*gridj->sy < by0)
+ {
+ d2zxy += gmx::square(gridj->c0[YY] + (cy+1)*gridj->sy - by0);
+ }
+ if (c1 > c0 && d2zxy < rl2)
+ {
+ cs = c0 + static_cast<int>(bz1_frac*(c1 - c0));
+ if (cs >= c1)
+ {
+ cs = c1 - 1;
+ }
+
+ d2xy = d2zxy - d2z;
+
+ /* Find the lowest cell that can possibly
+ * be within range.
+ */
+ cf = cs;
+ while (cf > c0 &&
+ (bbcz_j[cf*NNBSBB_D+1] >= bz0 ||
+ d2xy + gmx::square(bbcz_j[cf*NNBSBB_D+1] - bz0) < rl2))
+ {
+ cf--;
+ }
+
+ /* Find the highest cell that can possibly
+ * be within range.
+ */
+ cl = cs;
+ while (cl < c1-1 &&
+ (bbcz_j[cl*NNBSBB_D] <= bz1 ||
+ d2xy + gmx::square(bbcz_j[cl*NNBSBB_D] - bz1) < rl2))
+ {
+ cl++;
+ }
+
+#ifdef NBNXN_REFCODE
+ {
+ /* Simple reference code, for debugging,
+ * overrides the more complex code above.
+ */
+ cf = c1;
+ cl = -1;
+ for (int k = c0; k < c1; k++)
+ {
+ if (box_dist2(bx0, bx1, by0, by1, bz0, bz1, bb+k) < rl2 &&
+ k < cf)
+ {
+ cf = k;
+ }
+ if (box_dist2(bx0, bx1, by0, by1, bz0, bz1, bb+k) < rl2 &&
+ k > cl)
+ {
+ cl = k;
+ }
+ }
+ }
+#endif
+
+ if (gridi == gridj)
+ {
+ /* We want each atom/cell pair only once,
+ * only use cj >= ci.
+ */
+#ifndef NBNXN_SHIFT_BACKWARD
+ cf = std::max(cf, ci);
+#else
+ if (shift == CENTRAL)
+ {
+ cf = std::max(cf, ci);
+ }
+#endif
+ }
+
+ if (cf <= cl)
+ {
+ /* For f buffer flags with simple lists */
+ ncj_old_j = nbl->ncj;
+
+ switch (nb_kernel_type)
+ {
+ case nbnxnk4x4_PlainC:
+ check_cell_list_space_simple(nbl, cl-cf+1);
+
+ make_cluster_list_simple(gridj,
+ nbl, ci, cf, cl,
+ (gridi == gridj && shift == CENTRAL),
+ nbat->x,
+ rl2, rbb2,
+ &ndistc);
+ break;
+#ifdef GMX_NBNXN_SIMD_4XN
+ case nbnxnk4xN_SIMD_4xN:
+ check_cell_list_space_simple(nbl, ci_to_cj(na_cj_2log, cl-cf)+2);
+ make_cluster_list_simd_4xn(gridj,
+ nbl, ci, cf, cl,
+ (gridi == gridj && shift == CENTRAL),
+ nbat->x,
+ rl2, rbb2,
+ &ndistc);
+ break;
+#endif
+#ifdef GMX_NBNXN_SIMD_2XNN
+ case nbnxnk4xN_SIMD_2xNN:
+ check_cell_list_space_simple(nbl, ci_to_cj(na_cj_2log, cl-cf)+2);
+ make_cluster_list_simd_2xnn(gridj,
+ nbl, ci, cf, cl,
+ (gridi == gridj && shift == CENTRAL),
+ nbat->x,
+ rl2, rbb2,
+ &ndistc);
+ break;
+#endif
+ case nbnxnk8x8x8_PlainC:
+ case nbnxnk8x8x8_GPU:
+ check_cell_list_space_supersub(nbl, cl-cf+1);
+ for (cj = cf; cj <= cl; cj++)
+ {
+ make_cluster_list_supersub(gridi, gridj,
+ nbl, ci, cj,
+ (gridi == gridj && shift == CENTRAL && ci == cj),
+ nbat->xstride, nbat->x,
+ rl2, rbb2,
+ &ndistc);
+ }
+ break;
+ }
+ ncpcheck += cl - cf + 1;
+
+ if (bFBufferFlag && nbl->ncj > ncj_old_j)
+ {
+ int cbf = nbl->cj[ncj_old_j].cj >> gridj_flag_shift;
+ int cbl = nbl->cj[nbl->ncj-1].cj >> gridj_flag_shift;
+ for (int cb = cbf; cb <= cbl; cb++)
+ {
+ bitmask_init_bit(&gridj_flag[cb], th);
+ }
+ }
+ }
+ }
+ }
+ }
+
+ /* Set the exclusions for this ci list */
+ if (nbl->bSimple)
+ {
+ set_ci_top_excls(nbs,
+ nbl,
+ shift == CENTRAL && gridi == gridj,
+ gridj->na_c_2log,
+ na_cj_2log,
+ &(nbl->ci[nbl->nci]),
+ excl);
+
+ if (nbs->bFEP)
+ {
+ make_fep_list(nbs, nbat, nbl,
+ shift == CENTRAL && gridi == gridj,
+ &(nbl->ci[nbl->nci]),
+ gridi, gridj, nbl_fep);
+ }
+ }
+ else
+ {
+ set_sci_top_excls(nbs,
+ nbl,
+ shift == CENTRAL && gridi == gridj,
+ gridj->na_c_2log,
+ &(nbl->sci[nbl->nsci]),
+ excl);
+
+ if (nbs->bFEP)
+ {
+ make_fep_list_supersub(nbs, nbat, nbl,
+ shift == CENTRAL && gridi == gridj,
+ &(nbl->sci[nbl->nsci]),
+ shx, shy, shz,
+ rl_fep2,
+ gridi, gridj, nbl_fep);
+ }
+ }
+
+ /* Close this ci list */
+ if (nbl->bSimple)
+ {
+ close_ci_entry_simple(nbl);
+ }
+ else
+ {
+ close_ci_entry_supersub(nbl,
+ nsubpair_max,
+ progBal, nsubpair_tot_est,
+ th, nth);
+ }
+ }
+ }
+ }
+
+ if (bFBufferFlag && nbl->ncj > ncj_old_i)
+ {
+ bitmask_init_bit(&(work->buffer_flags.flag[(gridi->cell0+ci)>>gridi_flag_shift]), th);
+ }
+ }
+
+ work->ndistc = ndistc;
+
+ nbs_cycle_stop(&work->cc[enbsCCsearch]);
+
+ if (debug)
+ {
+ fprintf(debug, "number of distance checks %d\n", ndistc);
+ fprintf(debug, "ncpcheck %s %d\n", gridi == gridj ? "local" : "non-local",
+ ncpcheck);
+
+ if (nbl->bSimple)
+ {
+ print_nblist_statistics_simple(debug, nbl, nbs, rlist);
+ }
+ else
+ {
+ print_nblist_statistics_supersub(debug, nbl, nbs, rlist);
+ }
+
+ if (nbs->bFEP)
+ {
+ fprintf(debug, "nbl FEP list pairs: %d\n", nbl_fep->nrj);
+ }
+ }
+}
+
+static void reduce_buffer_flags(const nbnxn_search_t nbs,
+ int nsrc,
+ const nbnxn_buffer_flags_t *dest)
+{
+ for (int s = 0; s < nsrc; s++)
+ {
+ gmx_bitmask_t * flag = nbs->work[s].buffer_flags.flag;
+
+ for (int b = 0; b < dest->nflag; b++)
+ {
+ bitmask_union(&(dest->flag[b]), flag[b]);
+ }
+ }
+}
+
+static void print_reduction_cost(const nbnxn_buffer_flags_t *flags, int nout)
+{
+ int nelem, nkeep, ncopy, nred, out;
+ gmx_bitmask_t mask_0;
+
+ nelem = 0;
+ nkeep = 0;
+ ncopy = 0;
+ nred = 0;
+ bitmask_init_bit(&mask_0, 0);
+ for (int b = 0; b < flags->nflag; b++)
+ {
+ if (bitmask_is_equal(flags->flag[b], mask_0))
+ {
+ /* Only flag 0 is set, no copy of reduction required */
+ nelem++;
+ nkeep++;
+ }
+ else if (!bitmask_is_zero(flags->flag[b]))
+ {
+ int c = 0;
+ for (out = 0; out < nout; out++)
+ {
+ if (bitmask_is_set(flags->flag[b], out))
+ {
+ c++;
+ }
+ }
+ nelem += c;
+ if (c == 1)
+ {
+ ncopy++;
+ }
+ else
+ {
+ nred += c;
+ }
+ }
+ }
+
+ fprintf(debug, "nbnxn reduction: #flag %d #list %d elem %4.2f, keep %4.2f copy %4.2f red %4.2f\n",
+ flags->nflag, nout,
+ nelem/(double)(flags->nflag),
+ nkeep/(double)(flags->nflag),
+ ncopy/(double)(flags->nflag),
+ nred/(double)(flags->nflag));
+}
+
+/* Perform a count (linear) sort to sort the smaller lists to the end.
+ * This avoids load imbalance on the GPU, as large lists will be
+ * scheduled and executed first and the smaller lists later.
+ * Load balancing between multi-processors only happens at the end
+ * and there smaller lists lead to more effective load balancing.
+ * The sorting is done on the cj4 count, not on the actual pair counts.
+ * Not only does this make the sort faster, but it also results in
+ * better load balancing than using a list sorted on exact load.
+ * This function swaps the pointer in the pair list to avoid a copy operation.
+ */
+static void sort_sci(nbnxn_pairlist_t *nbl)
+{
+ nbnxn_list_work_t *work;
+ int m, s0, s1;
+ nbnxn_sci_t *sci_sort;
+
+ if (nbl->ncj4 <= nbl->nsci)
+ {
+ /* nsci = 0 or all sci have size 1, sorting won't change the order */
+ return;
+ }
+
+ work = nbl->work;
+
+ /* We will distinguish differences up to double the average */
+ m = (2*nbl->ncj4)/nbl->nsci;
+
+ if (m + 1 > work->sort_nalloc)
+ {
+ work->sort_nalloc = over_alloc_large(m + 1);
+ srenew(work->sort, work->sort_nalloc);
+ }
+
+ if (work->sci_sort_nalloc != nbl->sci_nalloc)
+ {
+ work->sci_sort_nalloc = nbl->sci_nalloc;
+ nbnxn_realloc_void((void **)&work->sci_sort,
+ 0,
+ work->sci_sort_nalloc*sizeof(*work->sci_sort),
+ nbl->alloc, nbl->free);
+ }
+
+ /* Count the entries of each size */
+ for (int i = 0; i <= m; i++)
+ {
+ work->sort[i] = 0;
+ }
+ for (int s = 0; s < nbl->nsci; s++)
+ {
+ int i = std::min(m, nbl->sci[s].cj4_ind_end - nbl->sci[s].cj4_ind_start);
+ work->sort[i]++;
+ }
+ /* Calculate the offset for each count */
+ s0 = work->sort[m];
+ work->sort[m] = 0;
+ for (int i = m - 1; i >= 0; i--)
+ {
+ s1 = work->sort[i];
+ work->sort[i] = work->sort[i + 1] + s0;
+ s0 = s1;
+ }
+
+ /* Sort entries directly into place */
+ sci_sort = work->sci_sort;
+ for (int s = 0; s < nbl->nsci; s++)
+ {
+ int i = std::min(m, nbl->sci[s].cj4_ind_end - nbl->sci[s].cj4_ind_start);
+ sci_sort[work->sort[i]++] = nbl->sci[s];
+ }
+
+ /* Swap the sci pointers so we use the new, sorted list */
+ work->sci_sort = nbl->sci;
+ nbl->sci = sci_sort;
+}
+
+/* Make a local or non-local pair-list, depending on iloc */
+void nbnxn_make_pairlist(const nbnxn_search_t nbs,
+ nbnxn_atomdata_t *nbat,
+ const t_blocka *excl,
+ real rlist,
+ int min_ci_balanced,
+ nbnxn_pairlist_set_t *nbl_list,
+ int iloc,
+ int nb_kernel_type,
+ t_nrnb *nrnb)
+{
+ nbnxn_grid_t *gridi, *gridj;
+ gmx_bool bGPUCPU;
+ int nzi, zj0, zj1;
+ int nsubpair_target, nsubpair_tot_est;
+ int nnbl;
+ nbnxn_pairlist_t **nbl;
+ int ci_block;
+ gmx_bool CombineNBLists;
+ gmx_bool progBal;
+ int np_tot, np_noq, np_hlj, nap;
+
+ /* Check if we are running hybrid GPU + CPU nbnxn mode */
+ bGPUCPU = (!nbs->grid[0].bSimple && nbl_list->bSimple);
+
+ nnbl = nbl_list->nnbl;
+ nbl = nbl_list->nbl;
+ CombineNBLists = nbl_list->bCombined;
+
+ if (debug)
+ {
+ fprintf(debug, "ns making %d nblists\n", nnbl);
+ }
+
+ nbat->bUseBufferFlags = (nbat->nout > 1);
+ /* We should re-init the flags before making the first list */
+ if (nbat->bUseBufferFlags && (LOCAL_I(iloc) || bGPUCPU))
+ {
+ init_buffer_flags(&nbat->buffer_flags, nbat->natoms);
+ }
+
+ if (nbl_list->bSimple)
+ {
+#if GMX_SIMD
+ switch (nb_kernel_type)
+ {
+#ifdef GMX_NBNXN_SIMD_4XN
+ case nbnxnk4xN_SIMD_4xN:
+ nbs->icell_set_x = icell_set_x_simd_4xn;
+ break;
+#endif
+#ifdef GMX_NBNXN_SIMD_2XNN
+ case nbnxnk4xN_SIMD_2xNN:
+ nbs->icell_set_x = icell_set_x_simd_2xnn;
+ break;
+#endif
+ default:
+ nbs->icell_set_x = icell_set_x_simple;
+ break;
+ }
+#else // GMX_SIMD
+ /* MSVC 2013 complains about switch statements without case */
+ nbs->icell_set_x = icell_set_x_simple;
+#endif // GMX_SIMD
+ }
+ else
+ {
+ nbs->icell_set_x = icell_set_x_supersub;
+ }
+
+ if (LOCAL_I(iloc))
+ {
+ /* Only zone (grid) 0 vs 0 */
+ nzi = 1;
+ zj0 = 0;
+ zj1 = 1;
+ }
+ else
+ {
+ nzi = nbs->zones->nizone;
+ }
+
+ if (!nbl_list->bSimple && min_ci_balanced > 0)
+ {
+ get_nsubpair_target(nbs, iloc, rlist, min_ci_balanced,
+ &nsubpair_target, &nsubpair_tot_est);
+ }
+ else
+ {
+ nsubpair_target = 0;
+ nsubpair_tot_est = 0;
+ }
+
+ /* Clear all pair-lists */
+ for (int th = 0; th < nnbl; th++)
+ {
+ clear_pairlist(nbl[th]);
+
+ if (nbs->bFEP)
+ {
+ clear_pairlist_fep(nbl_list->nbl_fep[th]);
+ }
+ }
+
+ for (int zi = 0; zi < nzi; zi++)
+ {
+ gridi = &nbs->grid[zi];
+
+ if (NONLOCAL_I(iloc))
+ {
+ zj0 = nbs->zones->izone[zi].j0;
+ zj1 = nbs->zones->izone[zi].j1;
+ if (zi == 0)
+ {
+ zj0++;
+ }
+ }
+ for (int zj = zj0; zj < zj1; zj++)
+ {
+ gridj = &nbs->grid[zj];
+
+ if (debug)
+ {
+ fprintf(debug, "ns search grid %d vs %d\n", zi, zj);
+ }
+
+ nbs_cycle_start(&nbs->cc[enbsCCsearch]);
+
+ if (nbl[0]->bSimple && !gridi->bSimple)
+ {
+ /* Hybrid list, determine blocking later */
+ ci_block = 0;
+ }
+ else
+ {
+ ci_block = get_ci_block_size(gridi, nbs->DomDec, nnbl);
+ }
+
+ /* With GPU: generate progressively smaller lists for
+ * load balancing for local only or non-local with 2 zones.
+ */
+ progBal = (LOCAL_I(iloc) || nbs->zones->n <= 2);
+
+#pragma omp parallel for num_threads(nnbl) schedule(static)
+ for (int th = 0; th < nnbl; th++)
+ {
+ try
+ {
+ /* Re-init the thread-local work flag data before making
+ * the first list (not an elegant conditional).
+ */
+ if (nbat->bUseBufferFlags && ((zi == 0 && zj == 0) ||
+ (bGPUCPU && zi == 0 && zj == 1)))
+ {
+ init_buffer_flags(&nbs->work[th].buffer_flags, nbat->natoms);
+ }
+
+ if (CombineNBLists && th > 0)
+ {
+ clear_pairlist(nbl[th]);
+ }
+
+ /* Divide the i super cell equally over the nblists */
+ nbnxn_make_pairlist_part(nbs, gridi, gridj,
+ &nbs->work[th], nbat, excl,
+ rlist,
+ nb_kernel_type,
+ ci_block,
+ nbat->bUseBufferFlags,
+ nsubpair_target,
+ progBal, nsubpair_tot_est,
+ th, nnbl,
+ nbl[th],
+ nbl_list->nbl_fep[th]);
+ }
+ GMX_CATCH_ALL_AND_EXIT_WITH_FATAL_ERROR;
+ }
+ nbs_cycle_stop(&nbs->cc[enbsCCsearch]);
+
+ np_tot = 0;
+ np_noq = 0;
+ np_hlj = 0;
+ for (int th = 0; th < nnbl; th++)
+ {
+ inc_nrnb(nrnb, eNR_NBNXN_DIST2, nbs->work[th].ndistc);
+
+ if (nbl_list->bSimple)
+ {
+ np_tot += nbl[th]->ncj;
+ np_noq += nbl[th]->work->ncj_noq;
+ np_hlj += nbl[th]->work->ncj_hlj;
+ }
+ else
+ {
+ /* This count ignores potential subsequent pair pruning */
+ np_tot += nbl[th]->nci_tot;
+ }
+ }
+ nap = nbl[0]->na_ci*nbl[0]->na_cj;
+ nbl_list->natpair_ljq = (np_tot - np_noq)*nap - np_hlj*nap/2;
+ nbl_list->natpair_lj = np_noq*nap;
+ nbl_list->natpair_q = np_hlj*nap/2;
+
+ if (CombineNBLists && nnbl > 1)
+ {
+ nbs_cycle_start(&nbs->cc[enbsCCcombine]);
+
+ combine_nblists(nnbl-1, nbl+1, nbl[0]);
+
+ nbs_cycle_stop(&nbs->cc[enbsCCcombine]);
+ }
+ }
+ }
+
+ if (!nbl_list->bSimple)
+ {
+ /* Sort the entries on size, large ones first */
+ if (CombineNBLists || nnbl == 1)
+ {
+ sort_sci(nbl[0]);
+ }
+ else
+ {
+#pragma omp parallel for num_threads(nnbl) schedule(static)
+ for (int th = 0; th < nnbl; th++)
+ {
+ try
+ {
+ sort_sci(nbl[th]);
+ }
+ GMX_CATCH_ALL_AND_EXIT_WITH_FATAL_ERROR;
+ }
+ }
+ }
+
+ if (nbat->bUseBufferFlags)
+ {
+ reduce_buffer_flags(nbs, nnbl, &nbat->buffer_flags);
+ }
+
+ if (nbs->bFEP)
+ {
+ /* Balance the free-energy lists over all the threads */
+ balance_fep_lists(nbs, nbl_list);
+ }
+
+ /* Special performance logging stuff (env.var. GMX_NBNXN_CYCLE) */
+ if (LOCAL_I(iloc))
+ {
+ nbs->search_count++;
+ }
+ if (nbs->print_cycles &&
+ (!nbs->DomDec || (nbs->DomDec && !LOCAL_I(iloc))) &&
+ nbs->search_count % 100 == 0)
+ {
+ nbs_cycle_print(stderr, nbs);
+ }
+
+ if (debug && (CombineNBLists && nnbl > 1))
+ {
+ if (nbl[0]->bSimple)
+ {
+ print_nblist_statistics_simple(debug, nbl[0], nbs, rlist);
+ }
+ else
+ {
+ print_nblist_statistics_supersub(debug, nbl[0], nbs, rlist);
+ }
+ }
+
+ if (debug)
+ {
+ if (gmx_debug_at)
+ {
+ if (nbl[0]->bSimple)
+ {
+ print_nblist_ci_cj(debug, nbl[0]);
+ }
+ else
+ {
+ print_nblist_sci_cj(debug, nbl[0]);
+ }
+ }
+
+ if (nbat->bUseBufferFlags)
+ {
+ print_reduction_cost(&nbat->buffer_flags, nnbl);
+ }
+ }
+}
biod.pnpi.spb.ru / alexxy / gromacs.git / commitdiff