impl_->title_ = title;
}
+void
+AbstractPlotModule::setTitle(const std::string &title)
+{
+ impl_->title_ = title;
+}
+
void
AbstractPlotModule::setSubtitle(const char *subtitle)
}
+void
+AbstractPlotModule::setSubtitle(const std::string &subtitle)
+{
+ impl_->subtitle_ = subtitle;
+}
+
+
void
AbstractPlotModule::setXLabel(const char *label)
{
* Set plot title.
*/
void setTitle(const char *title);
+ //! \copydoc setTitle(const char *)
+ void setTitle(const std::string &title);
/*! \brief
* Set plot subtitle.
*/
void setSubtitle(const char *subtitle);
+ //! \copydoc setSubtitle(const char *)
+ void setSubtitle(const std::string &subtitle);
/*! \brief
* Set X axis label.
*/
int
gmx_rama(int argc, char *argv[]);
-int
-gmx_rdf(int argc, char *argv[]);
-
int
gmx_rotmat(int argc, char *argv[]);
+++ /dev/null
-/*
- * This file is part of the GROMACS molecular simulation package.
- *
- * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
- * Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014, by the GROMACS development team, led by
- * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
- * and including many others, as listed in the AUTHORS file in the
- * top-level source directory and at http://www.gromacs.org.
- *
- * GROMACS is free software; you can redistribute it and/or
- * modify it under the terms of the GNU Lesser General Public License
- * as published by the Free Software Foundation; either version 2.1
- * of the License, or (at your option) any later version.
- *
- * GROMACS is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
- * Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public
- * License along with GROMACS; if not, see
- * http://www.gnu.org/licenses, or write to the Free Software Foundation,
- * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
- *
- * If you want to redistribute modifications to GROMACS, please
- * consider that scientific software is very special. Version
- * control is crucial - bugs must be traceable. We will be happy to
- * consider code for inclusion in the official distribution, but
- * derived work must not be called official GROMACS. Details are found
- * in the README & COPYING files - if they are missing, get the
- * official version at http://www.gromacs.org.
- *
- * To help us fund GROMACS development, we humbly ask that you cite
- * the research papers on the package. Check out http://www.gromacs.org.
- */
-
-#include "gmxpre.h"
-
-#include <math.h>
-
-#include "gromacs/commandline/pargs.h"
-#include "gromacs/correlationfunctions/integrate.h"
-#include "gromacs/fileio/tpxio.h"
-#include "gromacs/fileio/trxio.h"
-#include "gromacs/fileio/xvgr.h"
-#include "gromacs/gmxana/gmx_ana.h"
-#include "gromacs/gmxana/gstat.h"
-#include "gromacs/legacyheaders/macros.h"
-#include "gromacs/legacyheaders/names.h"
-#include "gromacs/legacyheaders/nrnb.h"
-#include "gromacs/legacyheaders/typedefs.h"
-#include "gromacs/legacyheaders/viewit.h"
-#include "gromacs/math/vec.h"
-#include "gromacs/pbcutil/pbc.h"
-#include "gromacs/pbcutil/rmpbc.h"
-#include "gromacs/topology/index.h"
-#include "gromacs/utility/fatalerror.h"
-#include "gromacs/utility/futil.h"
-#include "gromacs/utility/smalloc.h"
-
-static void check_box_c(matrix box)
-{
- if (fabs(box[ZZ][XX]) > GMX_REAL_EPS*box[ZZ][ZZ] ||
- fabs(box[ZZ][YY]) > GMX_REAL_EPS*box[ZZ][ZZ])
- {
- gmx_fatal(FARGS,
- "The last box vector is not parallel to the z-axis: %f %f %f",
- box[ZZ][XX], box[ZZ][YY], box[ZZ][ZZ]);
- }
-}
-
-static void calc_comg(int is, int *coi, int *index, gmx_bool bMass, t_atom *atom,
- rvec *x, rvec *x_comg)
-{
- int c, i, d;
- rvec xc;
- real mtot, m;
-
- if (bMass && atom == NULL)
- {
- gmx_fatal(FARGS, "No masses available while mass weighting was requested");
- }
-
- for (c = 0; c < is; c++)
- {
- clear_rvec(xc);
- mtot = 0;
- for (i = coi[c]; i < coi[c+1]; i++)
- {
- if (bMass)
- {
- m = atom[index[i]].m;
- for (d = 0; d < DIM; d++)
- {
- xc[d] += m*x[index[i]][d];
- }
- mtot += m;
- }
- else
- {
- rvec_inc(xc, x[index[i]]);
- mtot += 1.0;
- }
- }
- svmul(1/mtot, xc, x_comg[c]);
- }
-}
-
-static void split_group(int isize, int *index, char *grpname,
- t_topology *top, char type,
- int *is_out, int **coi_out)
-{
- t_block *mols = NULL;
- t_atom *atom = NULL;
- int is, *coi;
- int cur, mol, res, i, a, i1;
-
- /* Split up the group in molecules or residues */
- switch (type)
- {
- case 'm':
- mols = &top->mols;
- break;
- case 'r':
- atom = top->atoms.atom;
- break;
- default:
- gmx_fatal(FARGS, "Unknown rdf option '%s'", type);
- }
- snew(coi, isize+1);
- is = 0;
- cur = -1;
- mol = 0;
- for (i = 0; i < isize; i++)
- {
- a = index[i];
- if (type == 'm')
- {
- /* Check if the molecule number has changed */
- i1 = mols->index[mol+1];
- while (a >= i1)
- {
- mol++;
- i1 = mols->index[mol+1];
- }
- if (mol != cur)
- {
- coi[is++] = i;
- cur = mol;
- }
- }
- else if (type == 'r')
- {
- /* Check if the residue index has changed */
- res = atom[a].resind;
- if (res != cur)
- {
- coi[is++] = i;
- cur = res;
- }
- }
- }
- coi[is] = i;
- srenew(coi, is+1);
- printf("Group '%s' of %d atoms consists of %d %s\n",
- grpname, isize, is,
- (type == 'm' ? "molecules" : "residues"));
-
- *is_out = is;
- *coi_out = coi;
-}
-
-static void do_rdf(const char *fnNDX, const char *fnTPS, const char *fnTRX,
- const char *fnRDF, const char *fnCNRDF, const char *fnHQ,
- gmx_bool bCM, const char *close,
- const char **rdft, gmx_bool bXY, gmx_bool bPBC, gmx_bool bNormalize,
- real cutoff, real binwidth, real fade, int ng,
- const output_env_t oenv)
-{
- FILE *fp;
- t_trxstatus *status;
- char outf1[STRLEN], outf2[STRLEN];
- char title[STRLEN], gtitle[STRLEN], refgt[30];
- int g, natoms, i, ii, j, k, nbin, j0, j1, n, nframes;
- int **count;
- char **grpname;
- int *isize, isize_cm = 0, nrdf = 0, max_i, isize0, isize_g;
- atom_id **index, *index_cm = NULL;
- gmx_int64_t *sum;
- real t, rmax2, cut2, r, r2, r2ii, invhbinw, normfac;
- real segvol, spherevol, prev_spherevol, **rdf;
- rvec *x, dx, *x0 = NULL, *x_i1, xi;
- real *inv_segvol, invvol, invvol_sum, rho;
- gmx_bool bClose, *bExcl, bTop, bNonSelfExcl;
- matrix box, box_pbc;
- int **npairs;
- atom_id ix, jx, ***pairs;
- t_topology *top = NULL;
- int ePBC = -1, ePBCrdf = -1;
- t_block *mols = NULL;
- t_blocka *excl;
- t_atom *atom = NULL;
- t_pbc pbc;
- gmx_rmpbc_t gpbc = NULL;
- int *is = NULL, **coi = NULL, cur, mol, i1, res, a;
-
- excl = NULL;
-
- bClose = (close[0] != 'n');
-
- if (fnTPS)
- {
- snew(top, 1);
- bTop = read_tps_conf(fnTPS, title, top, &ePBC, &x, NULL, box, TRUE);
- if (bTop && !(bCM || bClose))
- {
- /* get exclusions from topology */
- excl = &(top->excls);
- }
- }
- snew(grpname, ng+1);
- snew(isize, ng+1);
- snew(index, ng+1);
- fprintf(stderr, "\nSelect a reference group and %d group%s\n",
- ng, ng == 1 ? "" : "s");
- if (fnTPS)
- {
- get_index(&(top->atoms), fnNDX, ng+1, isize, index, grpname);
- atom = top->atoms.atom;
- }
- else
- {
- rd_index(fnNDX, ng+1, isize, index, grpname);
- }
-
- if (bCM || bClose)
- {
- snew(is, 1);
- snew(coi, 1);
- if (bClose)
- {
- split_group(isize[0], index[0], grpname[0], top, close[0], &is[0], &coi[0]);
- }
- }
- if (rdft[0][0] != 'a')
- {
- /* Split up all the groups in molecules or residues */
- srenew(is, ng+1);
- srenew(coi, ng+1);
- for (g = ((bCM || bClose) ? 1 : 0); g < ng+1; g++)
- {
- split_group(isize[g], index[g], grpname[g], top, rdft[0][0], &is[g], &coi[g]);
- }
- }
-
- if (bCM)
- {
- is[0] = 1;
- snew(coi[0], is[0]+1);
- coi[0][0] = 0;
- coi[0][1] = isize[0];
- isize0 = is[0];
- snew(x0, isize0);
- }
- else if (bClose || rdft[0][0] != 'a')
- {
- isize0 = is[0];
- snew(x0, isize0);
- }
- else
- {
- isize0 = isize[0];
- }
-
- natoms = read_first_x(oenv, &status, fnTRX, &t, &x, box);
- if (!natoms)
- {
- gmx_fatal(FARGS, "Could not read coordinates from statusfile\n");
- }
- if (fnTPS)
- {
- /* check with topology */
- if (natoms > top->atoms.nr)
- {
- gmx_fatal(FARGS, "Trajectory (%d atoms) does not match topology (%d atoms)",
- natoms, top->atoms.nr);
- }
- }
- /* check with index groups */
- for (i = 0; i < ng+1; i++)
- {
- for (j = 0; j < isize[i]; j++)
- {
- if (index[i][j] >= natoms)
- {
- gmx_fatal(FARGS, "Atom index (%d) in index group %s (%d atoms) larger "
- "than number of atoms in trajectory (%d atoms)",
- index[i][j], grpname[i], isize[i], natoms);
- }
- }
- }
-
- /* initialize some handy things */
- if (ePBC == -1)
- {
- ePBC = guess_ePBC(box);
- }
- copy_mat(box, box_pbc);
- if (bXY)
- {
- check_box_c(box);
- switch (ePBC)
- {
- case epbcXYZ:
- case epbcXY: ePBCrdf = epbcXY; break;
- case epbcNONE: ePBCrdf = epbcNONE; break;
- default:
- gmx_fatal(FARGS, "xy-rdf's are not supported for pbc type'%s'",
- EPBC(ePBC));
- break;
- }
- /* Make sure the z-height does not influence the cut-off */
- box_pbc[ZZ][ZZ] = 2*max(box[XX][XX], box[YY][YY]);
- }
- else
- {
- ePBCrdf = ePBC;
- }
- if (bPBC)
- {
- rmax2 = 0.99*0.99*max_cutoff2(bXY ? epbcXY : epbcXYZ, box_pbc);
- }
- else
- {
- rmax2 = sqr(3*max(box[XX][XX], max(box[YY][YY], box[ZZ][ZZ])));
- }
- if (debug)
- {
- fprintf(debug, "rmax2 = %g\n", rmax2);
- }
-
- /* We use the double amount of bins, so we can correctly
- * write the rdf and rdf_cn output at i*binwidth values.
- */
- nbin = (int)(sqrt(rmax2) * 2 / binwidth);
- invhbinw = 2.0 / binwidth;
- cut2 = sqr(cutoff);
-
- snew(count, ng);
- snew(pairs, ng);
- snew(npairs, ng);
-
- snew(bExcl, natoms);
- max_i = 0;
- for (g = 0; g < ng; g++)
- {
- if (isize[g+1] > max_i)
- {
- max_i = isize[g+1];
- }
-
- /* this is THE array */
- snew(count[g], nbin+1);
-
- /* make pairlist array for groups and exclusions */
- snew(pairs[g], isize[0]);
- snew(npairs[g], isize[0]);
- for (i = 0; i < isize[0]; i++)
- {
- /* We can only have exclusions with atomic rdfs */
- if (!(bCM || bClose || rdft[0][0] != 'a'))
- {
- ix = index[0][i];
- for (j = 0; j < natoms; j++)
- {
- bExcl[j] = FALSE;
- }
- /* exclusions? */
- if (excl)
- {
- for (j = excl->index[ix]; j < excl->index[ix+1]; j++)
- {
- bExcl[excl->a[j]] = TRUE;
- }
- }
- k = 0;
- snew(pairs[g][i], isize[g+1]);
- bNonSelfExcl = FALSE;
- for (j = 0; j < isize[g+1]; j++)
- {
- jx = index[g+1][j];
- if (!bExcl[jx])
- {
- pairs[g][i][k++] = jx;
- }
- else if (ix != jx)
- {
- /* Check if we have exclusions other than self exclusions */
- bNonSelfExcl = TRUE;
- }
- }
- if (bNonSelfExcl)
- {
- npairs[g][i] = k;
- srenew(pairs[g][i], npairs[g][i]);
- }
- else
- {
- /* Save a LOT of memory and some cpu cycles */
- npairs[g][i] = -1;
- sfree(pairs[g][i]);
- }
- }
- else
- {
- npairs[g][i] = -1;
- }
- }
- }
- sfree(bExcl);
-
- snew(x_i1, max_i);
- nframes = 0;
- invvol_sum = 0;
- if (bPBC && (NULL != top))
- {
- gpbc = gmx_rmpbc_init(&top->idef, ePBC, natoms);
- }
-
- do
- {
- /* Must init pbc every step because of pressure coupling */
- copy_mat(box, box_pbc);
- if (bPBC)
- {
- if (top != NULL)
- {
- gmx_rmpbc(gpbc, natoms, box, x);
- }
- if (bXY)
- {
- check_box_c(box);
- clear_rvec(box_pbc[ZZ]);
- }
- set_pbc(&pbc, ePBCrdf, box_pbc);
-
- if (bXY)
- {
- /* Set z-size to 1 so we get the surface iso the volume */
- box_pbc[ZZ][ZZ] = 1;
- }
- }
- invvol = 1/det(box_pbc);
- invvol_sum += invvol;
-
- if (bCM)
- {
- /* Calculate center of mass of the whole group */
- calc_comg(is[0], coi[0], index[0], TRUE, atom, x, x0);
- }
- else if (!bClose && rdft[0][0] != 'a')
- {
- calc_comg(is[0], coi[0], index[0], rdft[0][6] == 'm', atom, x, x0);
- }
-
- for (g = 0; g < ng; g++)
- {
- if (rdft[0][0] == 'a')
- {
- /* Copy the indexed coordinates to a continuous array */
- for (i = 0; i < isize[g+1]; i++)
- {
- copy_rvec(x[index[g+1][i]], x_i1[i]);
- }
- }
- else
- {
- /* Calculate the COMs/COGs and store in x_i1 */
- calc_comg(is[g+1], coi[g+1], index[g+1], rdft[0][6] == 'm', atom, x, x_i1);
- }
-
- for (i = 0; i < isize0; i++)
- {
- if (bClose)
- {
- /* Special loop, since we need to determine the minimum distance
- * over all selected atoms in the reference molecule/residue.
- */
- if (rdft[0][0] == 'a')
- {
- isize_g = isize[g+1];
- }
- else
- {
- isize_g = is[g+1];
- }
- for (j = 0; j < isize_g; j++)
- {
- r2 = 1e30;
- /* Loop over the selected atoms in the reference molecule */
- for (ii = coi[0][i]; ii < coi[0][i+1]; ii++)
- {
- if (bPBC)
- {
- pbc_dx(&pbc, x[index[0][ii]], x_i1[j], dx);
- }
- else
- {
- rvec_sub(x[index[0][ii]], x_i1[j], dx);
- }
- if (bXY)
- {
- r2ii = dx[XX]*dx[XX] + dx[YY]*dx[YY];
- }
- else
- {
- r2ii = iprod(dx, dx);
- }
- if (r2ii < r2)
- {
- r2 = r2ii;
- }
- }
- if (r2 > cut2 && r2 <= rmax2)
- {
- count[g][(int)(sqrt(r2)*invhbinw)]++;
- }
- }
- }
- else
- {
- /* Real rdf between points in space */
- if (bCM || rdft[0][0] != 'a')
- {
- copy_rvec(x0[i], xi);
- }
- else
- {
- copy_rvec(x[index[0][i]], xi);
- }
- if (rdft[0][0] == 'a' && npairs[g][i] >= 0)
- {
- /* Expensive loop, because of indexing */
- for (j = 0; j < npairs[g][i]; j++)
- {
- jx = pairs[g][i][j];
- if (bPBC)
- {
- pbc_dx(&pbc, xi, x[jx], dx);
- }
- else
- {
- rvec_sub(xi, x[jx], dx);
- }
-
- if (bXY)
- {
- r2 = dx[XX]*dx[XX] + dx[YY]*dx[YY];
- }
- else
- {
- r2 = iprod(dx, dx);
- }
- if (r2 > cut2 && r2 <= rmax2)
- {
- count[g][(int)(sqrt(r2)*invhbinw)]++;
- }
- }
- }
- else
- {
- /* Cheaper loop, no exclusions */
- if (rdft[0][0] == 'a')
- {
- isize_g = isize[g+1];
- }
- else
- {
- isize_g = is[g+1];
- }
- for (j = 0; j < isize_g; j++)
- {
- if (bPBC)
- {
- pbc_dx(&pbc, xi, x_i1[j], dx);
- }
- else
- {
- rvec_sub(xi, x_i1[j], dx);
- }
- if (bXY)
- {
- r2 = dx[XX]*dx[XX] + dx[YY]*dx[YY];
- }
- else
- {
- r2 = iprod(dx, dx);
- }
- if (r2 > cut2 && r2 <= rmax2)
- {
- count[g][(int)(sqrt(r2)*invhbinw)]++;
- }
- }
- }
- }
- }
- }
- nframes++;
- }
- while (read_next_x(oenv, status, &t, x, box));
- fprintf(stderr, "\n");
-
- if (bPBC && (NULL != top))
- {
- gmx_rmpbc_done(gpbc);
- }
-
- close_trj(status);
-
- sfree(x);
-
- /* Average volume */
- invvol = invvol_sum/nframes;
-
- /* Calculate volume of sphere segments or length of circle segments */
- snew(inv_segvol, (nbin+1)/2);
- prev_spherevol = 0;
- for (i = 0; (i < (nbin+1)/2); i++)
- {
- r = (i + 0.5)*binwidth;
- if (bXY)
- {
- spherevol = M_PI*r*r;
- }
- else
- {
- spherevol = (4.0/3.0)*M_PI*r*r*r;
- }
- segvol = spherevol-prev_spherevol;
- inv_segvol[i] = 1.0/segvol;
- prev_spherevol = spherevol;
- }
-
- snew(rdf, ng);
- for (g = 0; g < ng; g++)
- {
- /* We have to normalize by dividing by the number of frames */
- if (rdft[0][0] == 'a')
- {
- normfac = 1.0/(nframes*invvol*isize0*isize[g+1]);
- }
- else
- {
- normfac = 1.0/(nframes*invvol*isize0*is[g+1]);
- }
-
- /* Do the normalization */
- nrdf = max((nbin+1)/2, 1+2*fade/binwidth);
- snew(rdf[g], nrdf);
- for (i = 0; i < (nbin+1)/2; i++)
- {
- r = i*binwidth;
- if (i == 0)
- {
- j = count[g][0];
- }
- else
- {
- j = count[g][i*2-1] + count[g][i*2];
- }
- if ((fade > 0) && (r >= fade))
- {
- rdf[g][i] = 1 + (j*inv_segvol[i]*normfac-1)*exp(-16*sqr(r/fade-1));
- }
- else
- {
- if (bNormalize)
- {
- rdf[g][i] = j*inv_segvol[i]*normfac;
- }
- else
- {
- rdf[g][i] = j/(binwidth*isize0*nframes);
- }
- }
- }
- for (; (i < nrdf); i++)
- {
- rdf[g][i] = 1.0;
- }
- }
-
- if (rdft[0][0] == 'a')
- {
- sprintf(gtitle, "Radial distribution");
- }
- else
- {
- sprintf(gtitle, "Radial distribution of %s %s",
- rdft[0][0] == 'm' ? "molecule" : "residue",
- rdft[0][6] == 'm' ? "COM" : "COG");
- }
- fp = xvgropen(fnRDF, gtitle, "r", "", oenv);
- if (bCM)
- {
- sprintf(refgt, " %s", "COM");
- }
- else if (bClose)
- {
- sprintf(refgt, " closest atom in %s.", close);
- }
- else
- {
- sprintf(refgt, "%s", "");
- }
- if (ng == 1)
- {
- if (output_env_get_print_xvgr_codes(oenv))
- {
- fprintf(fp, "@ subtitle \"%s%s - %s\"\n", grpname[0], refgt, grpname[1]);
- }
- }
- else
- {
- if (output_env_get_print_xvgr_codes(oenv))
- {
- fprintf(fp, "@ subtitle \"reference %s%s\"\n", grpname[0], refgt);
- }
- xvgr_legend(fp, ng, (const char**)(grpname+1), oenv);
- }
- for (i = 0; (i < nrdf); i++)
- {
- fprintf(fp, "%10g", i*binwidth);
- for (g = 0; g < ng; g++)
- {
- fprintf(fp, " %10g", rdf[g][i]);
- }
- fprintf(fp, "\n");
- }
- gmx_ffclose(fp);
-
- do_view(oenv, fnRDF, NULL);
-
- /* h(Q) function: fourier transform of rdf */
- if (fnHQ)
- {
- int nhq = 401;
- real *hq, *integrand, Q;
-
- /* Get a better number density later! */
- rho = isize[1]*invvol;
- snew(hq, nhq);
- snew(integrand, nrdf);
- for (i = 0; (i < nhq); i++)
- {
- Q = i*0.5;
- integrand[0] = 0;
- for (j = 1; (j < nrdf); j++)
- {
- r = j*binwidth;
- integrand[j] = (Q == 0) ? 1.0 : sin(Q*r)/(Q*r);
- integrand[j] *= 4.0*M_PI*rho*r*r*(rdf[0][j]-1.0);
- }
- hq[i] = print_and_integrate(debug, nrdf, binwidth, integrand, NULL, 0);
- }
- fp = xvgropen(fnHQ, "h(Q)", "Q(/nm)", "h(Q)", oenv);
- for (i = 0; (i < nhq); i++)
- {
- fprintf(fp, "%10g %10g\n", i*0.5, hq[i]);
- }
- gmx_ffclose(fp);
- do_view(oenv, fnHQ, NULL);
- sfree(hq);
- sfree(integrand);
- }
-
- if (fnCNRDF)
- {
- normfac = 1.0/(isize0*nframes);
- fp = xvgropen(fnCNRDF, "Cumulative Number RDF", "r", "number", oenv);
- if (ng == 1)
- {
- if (output_env_get_print_xvgr_codes(oenv))
- {
- fprintf(fp, "@ subtitle \"%s-%s\"\n", grpname[0], grpname[1]);
- }
- }
- else
- {
- if (output_env_get_print_xvgr_codes(oenv))
- {
- fprintf(fp, "@ subtitle \"reference %s\"\n", grpname[0]);
- }
- xvgr_legend(fp, ng, (const char**)(grpname+1), oenv);
- }
- snew(sum, ng);
- for (i = 0; (i <= nbin/2); i++)
- {
- fprintf(fp, "%10g", i*binwidth);
- for (g = 0; g < ng; g++)
- {
- fprintf(fp, " %10g", (real)((double)sum[g]*normfac));
- if (i*2+1 < nbin)
- {
- sum[g] += count[g][i*2] + count[g][i*2+1];
- }
- }
- fprintf(fp, "\n");
- }
- gmx_ffclose(fp);
- sfree(sum);
-
- do_view(oenv, fnCNRDF, NULL);
- }
-
- for (g = 0; g < ng; g++)
- {
- sfree(rdf[g]);
- }
- sfree(rdf);
-}
-
-
-int gmx_rdf(int argc, char *argv[])
-{
- const char *desc[] = {
- "The structure of liquids can be studied by either neutron or X-ray",
- "scattering. The most common way to describe liquid structure is by a",
- "radial distribution function. However, this is not easy to obtain from",
- "a scattering experiment.[PAR]",
- "[THISMODULE] calculates radial distribution functions in different ways.",
- "The normal method is around a (set of) particle(s), the other methods",
- "are around the center of mass of a set of particles ([TT]-com[tt])",
- "or to the closest particle in a set ([TT]-surf[tt]).",
- "With all methods, the RDF can also be calculated around axes parallel",
- "to the [IT]z[it]-axis with option [TT]-xy[tt].",
- "With option [TT]-surf[tt] normalization can not be used.[PAR]",
- "The option [TT]-rdf[tt] sets the type of RDF to be computed.",
- "Default is for atoms or particles, but one can also select center",
- "of mass or geometry of molecules or residues. In all cases, only",
- "the atoms in the index groups are taken into account.",
- "For molecules and/or the center of mass option, a run input file",
- "is required.",
- "Weighting other than COM or COG can currently only be achieved",
- "by providing a run input file with different masses.",
- "Options [TT]-com[tt] and [TT]-surf[tt] also work in conjunction",
- "with [TT]-rdf[tt].[PAR]",
- "If a run input file is supplied ([TT]-s[tt]) and [TT]-rdf[tt] is set",
- "to [TT]atom[tt], exclusions defined",
- "in that file are taken into account when calculating the RDF.",
- "The option [TT]-cut[tt] is meant as an alternative way to avoid",
- "intramolecular peaks in the RDF plot.",
- "It is however better to supply a run input file with a higher number of",
- "exclusions. For e.g. benzene a topology, setting nrexcl to 5",
- "would eliminate all intramolecular contributions to the RDF.",
- "Note that all atoms in the selected groups are used, also the ones",
- "that don't have Lennard-Jones interactions.[PAR]",
- "Option [TT]-cn[tt] produces the cumulative number RDF,",
- "i.e. the average number of particles within a distance r.[PAR]"
- };
- static gmx_bool bCM = FALSE, bXY = FALSE, bPBC = TRUE, bNormalize = TRUE;
- static real cutoff = 0, binwidth = 0.002, fade = 0.0;
- static int ngroups = 1;
-
- static const char *closet[] = { NULL, "no", "mol", "res", NULL };
- static const char *rdft[] = { NULL, "atom", "mol_com", "mol_cog", "res_com", "res_cog", NULL };
-
- t_pargs pa[] = {
- { "-bin", FALSE, etREAL, {&binwidth},
- "Binwidth (nm)" },
- { "-com", FALSE, etBOOL, {&bCM},
- "RDF with respect to the center of mass of first group" },
- { "-surf", FALSE, etENUM, {closet},
- "RDF with respect to the surface of the first group" },
- { "-rdf", FALSE, etENUM, {rdft},
- "RDF type" },
- { "-pbc", FALSE, etBOOL, {&bPBC},
- "Use periodic boundary conditions for computing distances. Without PBC the maximum range will be three times the largest box edge." },
- { "-norm", FALSE, etBOOL, {&bNormalize},
- "Normalize for volume and density" },
- { "-xy", FALSE, etBOOL, {&bXY},
- "Use only the x and y components of the distance" },
- { "-cut", FALSE, etREAL, {&cutoff},
- "Shortest distance (nm) to be considered"},
- { "-ng", FALSE, etINT, {&ngroups},
- "Number of secondary groups to compute RDFs around a central group" },
- { "-fade", FALSE, etREAL, {&fade},
- "From this distance onwards the RDF is tranformed by g'(r) = 1 + [g(r)-1] exp(-(r/fade-1)^2 to make it go to 1 smoothly. If fade is 0.0 nothing is done." }
- };
-#define NPA asize(pa)
- const char *fnTPS, *fnNDX;
- output_env_t oenv;
-
- t_filenm fnm[] = {
- { efTRX, "-f", NULL, ffREAD },
- { efTPS, NULL, NULL, ffOPTRD },
- { efNDX, NULL, NULL, ffOPTRD },
- { efXVG, "-o", "rdf", ffWRITE },
- { efXVG, "-cn", "rdf_cn", ffOPTWR },
- { efXVG, "-hq", "hq", ffOPTWR },
- };
-#define NFILE asize(fnm)
- if (!parse_common_args(&argc, argv, PCA_CAN_VIEW | PCA_CAN_TIME,
- NFILE, fnm, NPA, pa, asize(desc), desc, 0, NULL, &oenv))
- {
- return 0;
- }
-
- if (bCM || closet[0][0] != 'n' || rdft[0][0] == 'm' || rdft[0][6] == 'm')
- {
- fnTPS = ftp2fn(efTPS, NFILE, fnm);
- }
- else
- {
- fnTPS = ftp2fn_null(efTPS, NFILE, fnm);
- }
- fnNDX = ftp2fn_null(efNDX, NFILE, fnm);
-
- if (!fnTPS && !fnNDX)
- {
- gmx_fatal(FARGS, "Neither index file nor topology file specified\n"
- "Nothing to do!");
- }
-
- if (closet[0][0] != 'n')
- {
- if (bCM)
- {
- gmx_fatal(FARGS, "Can not have both -com and -surf");
- }
- if (bNormalize)
- {
- fprintf(stderr, "Turning of normalization because of option -surf\n");
- bNormalize = FALSE;
- }
- }
-
- do_rdf(fnNDX, fnTPS, ftp2fn(efTRX, NFILE, fnm),
- opt2fn("-o", NFILE, fnm), opt2fn_null("-cn", NFILE, fnm),
- opt2fn_null("-hq", NFILE, fnm),
- bCM, closet[0], rdft, bXY, bPBC, bNormalize, cutoff, binwidth, fade, ngroups,
- oenv);
-
- return 0;
-}
#include "modules/distance.h"
#include "modules/freevolume.h"
#include "modules/pairdist.h"
+#include "modules/rdf.h"
#include "modules/sasa.h"
#include "modules/select.h"
registerModule<DistanceInfo>(manager, group);
registerModule<FreeVolumeInfo>(manager, group);
registerModule<PairDistanceInfo>(manager, group);
+ registerModule<RdfInfo>(manager, group);
registerModule<SasaInfo>(manager, group);
registerModule<SelectInfo>(manager, group);
}
--- /dev/null
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
+ * Copyright (c) 2001-2004, The GROMACS development team.
+ * Copyright (c) 2013,2014, by the GROMACS development team, led by
+ * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+ * and including many others, as listed in the AUTHORS file in the
+ * top-level source directory and at http://www.gromacs.org.
+ *
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
+ * of the License, or (at your option) any later version.
+ *
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+ *
+ * If you want to redistribute modifications to GROMACS, please
+ * consider that scientific software is very special. Version
+ * control is crucial - bugs must be traceable. We will be happy to
+ * consider code for inclusion in the official distribution, but
+ * derived work must not be called official GROMACS. Details are found
+ * in the README & COPYING files - if they are missing, get the
+ * official version at http://www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the research papers on the package. Check out http://www.gromacs.org.
+ */
+/*! \internal \file
+ * \brief
+ * Implements gmx::analysismodules::Rdf.
+ *
+ * \author Teemu Murtola <teemu.murtola@gmail.com> (C++ conversion)
+ * \ingroup module_trajectoryanalysis
+ */
+#include "gmxpre.h"
+
+#include "rdf.h"
+
+#include <cmath>
+
+#include <algorithm>
+#include <limits>
+#include <string>
+#include <vector>
+
+#include "gromacs/analysisdata/analysisdata.h"
+#include "gromacs/analysisdata/modules/average.h"
+#include "gromacs/analysisdata/modules/histogram.h"
+#include "gromacs/analysisdata/modules/plot.h"
+#include "gromacs/fileio/trx.h"
+#include "gromacs/math/utilities.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/options/basicoptions.h"
+#include "gromacs/options/filenameoption.h"
+#include "gromacs/options/options.h"
+#include "gromacs/pbcutil/pbc.h"
+#include "gromacs/selection/nbsearch.h"
+#include "gromacs/selection/selection.h"
+#include "gromacs/selection/selectionoption.h"
+#include "gromacs/topology/topology.h"
+#include "gromacs/trajectoryanalysis/analysismodule.h"
+#include "gromacs/trajectoryanalysis/analysissettings.h"
+#include "gromacs/utility/exceptions.h"
+#include "gromacs/utility/stringutil.h"
+
+namespace gmx
+{
+
+namespace analysismodules
+{
+
+namespace
+{
+
+//! \addtogroup module_trajectoryanalysis
+//! \{
+
+/********************************************************************
+ * Actual analysis module
+ */
+
+/*! \brief
+ * Implements `gmx rdf` trajectory analysis module.
+ */
+class Rdf : public TrajectoryAnalysisModule
+{
+ public:
+ Rdf();
+
+ virtual void initOptions(Options *options,
+ TrajectoryAnalysisSettings *settings);
+ virtual void optionsFinished(Options *options,
+ TrajectoryAnalysisSettings *settings);
+ virtual void initAnalysis(const TrajectoryAnalysisSettings &settings,
+ const TopologyInformation &top);
+ virtual void initAfterFirstFrame(const TrajectoryAnalysisSettings &settings,
+ const t_trxframe &fr);
+
+ virtual TrajectoryAnalysisModuleDataPointer startFrames(
+ const AnalysisDataParallelOptions &opt,
+ const SelectionCollection &selections);
+ virtual void analyzeFrame(int frnr, const t_trxframe &fr, t_pbc *pbc,
+ TrajectoryAnalysisModuleData *pdata);
+
+ virtual void finishAnalysis(int nframes);
+ virtual void writeOutput();
+
+ private:
+ std::string fnRdf_;
+ std::string fnCumulative_;
+ std::string surface_;
+ AnalysisDataPlotSettings plotSettings_;
+
+ /*! \brief
+ * Reference selection to compute RDFs around.
+ *
+ * With -surf, Selection::originalIds() and Selection::mappedIds()
+ * store the index of the surface group to which that position belongs.
+ * The RDF is computed by finding the nearest position from each
+ * surface group for each position, and then binning those distances.
+ */
+ Selection refSel_;
+ /*! \brief
+ * Selections to compute RDFs for.
+ */
+ SelectionList sel_;
+
+ /*! \brief
+ * Raw pairwise distance data from which the RDF is computed.
+ *
+ * There is a data set for each selection in `sel_`, with a single
+ * column. Each point set will contain a single pairwise distance
+ * that contributes to the RDF.
+ */
+ AnalysisData pairDist_;
+ /*! \brief
+ * Normalization factors for each frame.
+ *
+ * The first column contains the number of positions in `refSel_` for
+ * that frame (with surface RDF, the number of groups). There are
+ * `sel_.size()` more columns, each containing the number density of
+ * positions for one selection.
+ */
+ AnalysisData normFactors_;
+ /*! \brief
+ * Histogram module that computes the actual RDF from `pairDist_`.
+ *
+ * The per-frame histograms are raw pair counts in each bin;
+ * the averager is normalized by the average number of reference
+ * positions (average of the first column of `normFactors_`).
+ */
+ AnalysisDataSimpleHistogramModulePointer pairCounts_;
+ /*! \brief
+ * Average normalization factors.
+ */
+ AnalysisDataAverageModulePointer normAve_;
+ //! Neighborhood search with `refSel_` as the reference positions.
+ AnalysisNeighborhood nb_;
+
+ // User input options.
+ double binwidth_;
+ double cutoff_;
+ double rmax_;
+ bool bNormalize_;
+ bool bXY_;
+ bool bExclusions_;
+
+ // Pre-computed values for faster access during analysis.
+ real cut2_;
+ real rmax2_;
+ int surfaceGroupCount_;
+
+ // Copy and assign disallowed by base.
+};
+
+Rdf::Rdf()
+ : TrajectoryAnalysisModule(RdfInfo::name, RdfInfo::shortDescription),
+ pairCounts_(new AnalysisDataSimpleHistogramModule()),
+ normAve_(new AnalysisDataAverageModule()),
+ binwidth_(0.002), cutoff_(0.0), rmax_(0.0),
+ bNormalize_(true), bXY_(false), bExclusions_(false),
+ cut2_(0.0), rmax2_(0.0), surfaceGroupCount_(0)
+{
+ pairDist_.setMultipoint(true);
+ pairDist_.addModule(pairCounts_);
+ registerAnalysisDataset(&pairDist_, "pairdist");
+ registerBasicDataset(pairCounts_.get(), "paircount");
+
+ normFactors_.addModule(normAve_);
+ registerAnalysisDataset(&normFactors_, "norm");
+}
+
+void
+Rdf::initOptions(Options *options, TrajectoryAnalysisSettings * /*settings*/)
+{
+ static const char *const desc[] = {
+ "[THISMODULE] calculates radial distribution functions from one",
+ "refernce set of position (set with [TT]-ref[tt]) to one or more",
+ "sets of positions (set with [TT]-sel[tt]). To compute the RDF with",
+ "respect to the closest position in a set in [TT]-ref[tt] instead, use",
+ "[TT]-surf[tt]: if set, then [TT]-ref[tt] is partitioned into sets",
+ "based on the value of [TT]-surf[tt], and the closest position in each",
+ "set is used. To compute the RDF around axes parallel to the",
+ "[IT]z[it]-axis, i.e., only in the [IT]x[it]-[IT]y[it] plane, use",
+ "[TT]-xy[tt].[PAR]",
+ "To set the bin width and maximum distance to use in the RDF, use",
+ "[TT]-bin[tt] and [TT]-rmax[tt], respectively. The latter can be",
+ "used to limit the computational cost if the RDF is not of interest",
+ "up to the default (half of the box size with PBC, three times the",
+ "box size without PBC).[PAR]",
+ "To use exclusions from the topology ([TT]-s[tt]), set [TT]-excl[tt]",
+ "and ensure that both [TT]-ref[tt] and [TT]-sel[tt] only select atoms.",
+ "A rougher alternative to exclude intra-molecular peaks is to set",
+ "[TT]-cut[tt] to a non-zero value to clear the RDF at small",
+ "distances.[PAR]",
+ "The RDFs are normalized by 1) average number of positions in",
+ "[TT]-ref[tt] (the number of groups with [TT]-surf[tt]), 2) volume",
+ "of the bin, and 3) average particle density of [TT]-sel[tt] positions",
+ "for that selection. To only use the first factor for normalization,",
+ "set [TT]-nonorm[tt]. In this case, the RDF is only scaled with the",
+ "bin width to make the integral of the curve represent the number of",
+ "pairs within a range. Note that exclusions do not affect the",
+ "normalization: even if [TT]-excl[tt] is set, or [TT]-ref[tt] and",
+ "[TT]-sel[tt] contain the same selection, the normalization factor",
+ "is still N*M, not N*(M-excluded).[PAR]",
+ "For [TT]-surf[tt], the selection provided to [TT]-ref[tt] must",
+ "select atoms, i.e., centers of mass are not supported. Further,",
+ "[TT]-nonorm[tt] is implied, as the bins have irregular shapes and",
+ "the volume of a bin is not easily computable.[PAR]",
+ "Option [TT]-cn[tt] produces the cumulative number RDF,",
+ "i.e. the average number of particles within a distance r.[PAR]"
+ };
+
+ options->setDescription(desc);
+
+ options->addOption(FileNameOption("o").filetype(eftPlot).outputFile().required()
+ .store(&fnRdf_).defaultBasename("rdf")
+ .description("Computed RDFs"));
+ options->addOption(FileNameOption("cn").filetype(eftPlot).outputFile()
+ .store(&fnCumulative_).defaultBasename("rdf_cn")
+ .description("Cumulative RDFs"));
+
+ options->addOption(DoubleOption("bin").store(&binwidth_)
+ .description("Bin width (nm)"));
+ options->addOption(BooleanOption("norm").store(&bNormalize_)
+ .description("Normalize for bin volume and density"));
+ options->addOption(BooleanOption("xy").store(&bXY_)
+ .description("Use only the x and y components of the distance"));
+ options->addOption(BooleanOption("excl").store(&bExclusions_)
+ .description("Use exclusions from topology"));
+ options->addOption(DoubleOption("cut").store(&cutoff_)
+ .description("Shortest distance (nm) to be considered"));
+ options->addOption(DoubleOption("rmax").store(&rmax_)
+ .description("Largest distance (nm) to calculate"));
+
+ const char *const cSurfaceEnum[] = { "no", "mol", "res" };
+ options->addOption(StringOption("surf").enumValue(cSurfaceEnum)
+ .defaultEnumIndex(0).store(&surface_)
+ .description("RDF with respect to the surface of the reference"));
+
+ options->addOption(SelectionOption("ref").store(&refSel_).required()
+ .description("Reference selection for RDF computation"));
+ options->addOption(SelectionOption("sel").storeVector(&sel_)
+ .required().multiValue()
+ .description("Selections to compute RDFs for from the reference"));
+}
+
+void
+Rdf::optionsFinished(Options *options, TrajectoryAnalysisSettings *settings)
+{
+ if (surface_ != "no")
+ {
+ settings->setFlag(TrajectoryAnalysisSettings::efRequireTop);
+
+ if (options->isSet("norm") && bNormalize_)
+ {
+ GMX_THROW(InconsistentInputError("-surf cannot be combined with -norm"));
+ }
+ bNormalize_ = false;
+ if (bExclusions_)
+ {
+ GMX_THROW(InconsistentInputError("-surf cannot be combined with -excl"));
+ }
+ }
+ if (bExclusions_)
+ {
+ settings->setFlag(TrajectoryAnalysisSettings::efRequireTop);
+ }
+ if (cutoff_ < 0.0)
+ {
+ cutoff_ = 0.0;
+ }
+}
+
+void
+Rdf::initAnalysis(const TrajectoryAnalysisSettings &settings,
+ const TopologyInformation &top)
+{
+ pairDist_.setDataSetCount(sel_.size());
+ for (size_t i = 0; i < sel_.size(); ++i)
+ {
+ pairDist_.setColumnCount(i, 1);
+ }
+ plotSettings_ = settings.plotSettings();
+ nb_.setXYMode(bXY_);
+
+ normFactors_.setColumnCount(0, sel_.size() + 1);
+
+ const bool bSurface = (surface_ != "no");
+ if (bSurface)
+ {
+ if (!refSel_.hasOnlyAtoms())
+ {
+ GMX_THROW(InconsistentInputError("-surf only works with -refsel that consists of atoms"));
+ }
+ const e_index_t type = (surface_ == "mol" ? INDEX_MOL : INDEX_RES);
+ surfaceGroupCount_ = refSel_.initOriginalIdsToGroup(top.topology(), type);
+ }
+
+ if (bExclusions_)
+ {
+ if (!refSel_.hasOnlyAtoms())
+ {
+ GMX_THROW(InconsistentInputError("-excl only works with selections that consist of atoms"));
+ }
+ for (size_t i = 0; i < sel_.size(); ++i)
+ {
+ if (!sel_[i].hasOnlyAtoms())
+ {
+ GMX_THROW(InconsistentInputError("-excl only works with selections that consist of atoms"));
+ }
+ }
+ const t_topology *topology = top.topology();
+ if (topology->excls.nr == 0)
+ {
+ GMX_THROW(InconsistentInputError("-excl is set, but the file provided to -s does not define exclusions"));
+ }
+ nb_.setTopologyExclusions(&topology->excls);
+ }
+}
+
+void
+Rdf::initAfterFirstFrame(const TrajectoryAnalysisSettings &settings,
+ const t_trxframe &fr)
+{
+ // If -rmax is not provided, determine one from the box for the first frame.
+ if (rmax_ <= 0.0)
+ {
+ matrix box;
+ copy_mat(fr.box, box);
+ if (settings.hasPBC())
+ {
+ if (bXY_)
+ {
+ box[ZZ][ZZ] = 2*std::max(box[XX][XX], box[YY][YY]);
+ }
+ rmax_ = std::sqrt(0.99*0.99*max_cutoff2(bXY_ ? epbcXY : epbcXYZ, box));
+ }
+ else
+ {
+ if (bXY_)
+ {
+ clear_rvec(box[ZZ]);
+ }
+ rmax_ = 3*std::max(box[XX][XX], std::max(box[YY][YY], box[ZZ][ZZ]));
+ }
+ }
+ cut2_ = sqr(cutoff_);
+ rmax2_ = sqr(rmax_);
+ nb_.setCutoff(rmax_);
+ // We use the double amount of bins, so we can correctly
+ // write the rdf and rdf_cn output at i*binwidth values.
+ pairCounts_->init(histogramFromRange(0.0, rmax_).binWidth(binwidth_ / 2.0));
+}
+
+/*! \brief
+ * Temporary memory for use within a single-frame calculation.
+ */
+class RdfModuleData : public TrajectoryAnalysisModuleData
+{
+ public:
+ /*! \brief
+ * Reserves memory for the frame-local data.
+ *
+ * `surfaceGroupCount` will be zero if -surf is not specified.
+ */
+ RdfModuleData(TrajectoryAnalysisModule *module,
+ const AnalysisDataParallelOptions &opt,
+ const SelectionCollection &selections,
+ int surfaceGroupCount)
+ : TrajectoryAnalysisModuleData(module, opt, selections)
+ {
+ surfaceDist2_.resize(surfaceGroupCount);
+ }
+
+ virtual void finish() { finishDataHandles(); }
+
+ /*! \brief
+ * Minimum distance to each surface group.
+ *
+ * One entry for each group (residue/molecule, per -surf) in the
+ * reference selection.
+ * This is needed to support neighborhood searching, which may not
+ * return the reference positions in order: for each position, we need
+ * to search through all the reference positions and update this array
+ * to find the minimum distance to each surface group, and then compute
+ * the RDF from these numbers.
+ */
+ std::vector<real> surfaceDist2_;
+};
+
+TrajectoryAnalysisModuleDataPointer Rdf::startFrames(
+ const AnalysisDataParallelOptions &opt,
+ const SelectionCollection &selections)
+{
+ return TrajectoryAnalysisModuleDataPointer(
+ new RdfModuleData(this, opt, selections, surfaceGroupCount_));
+}
+
+void
+Rdf::analyzeFrame(int frnr, const t_trxframe &fr, t_pbc *pbc,
+ TrajectoryAnalysisModuleData *pdata)
+{
+ AnalysisDataHandle dh = pdata->dataHandle(pairDist_);
+ AnalysisDataHandle nh = pdata->dataHandle(normFactors_);
+ const Selection &refSel = pdata->parallelSelection(refSel_);
+ const SelectionList &sel = pdata->parallelSelections(sel_);
+ RdfModuleData &frameData = *static_cast<RdfModuleData *>(pdata);
+ const bool bSurface = !frameData.surfaceDist2_.empty();
+
+ matrix boxForVolume;
+ copy_mat(fr.box, boxForVolume);
+ if (bXY_)
+ {
+ // Set z-size to 1 so we get the surface are iso the volume
+ clear_rvec(boxForVolume[ZZ]);
+ boxForVolume[ZZ][ZZ] = 1;
+ }
+ const real inverseVolume = 1.0 / det(boxForVolume);
+
+ nh.startFrame(frnr, fr.time);
+ // Compute the normalization factor for the number of reference positions.
+ if (bSurface)
+ {
+ if (refSel.isDynamic())
+ {
+ // Count the number of distinct groups.
+ // This assumes that each group is continuous, which is currently
+ // the case.
+ int count = 0;
+ int prevId = -1;
+ for (int i = 0; i < refSel.posCount(); ++i)
+ {
+ const int id = refSel.position(i).mappedId();
+ if (id != prevId)
+ {
+ ++count;
+ prevId = id;
+ }
+ }
+ nh.setPoint(0, count);
+ }
+ else
+ {
+ nh.setPoint(0, surfaceGroupCount_);
+ }
+ }
+ else
+ {
+ nh.setPoint(0, refSel.posCount());
+ }
+
+ dh.startFrame(frnr, fr.time);
+ AnalysisNeighborhoodSearch nbsearch = nb_.initSearch(pbc, refSel);
+ for (size_t g = 0; g < sel.size(); ++g)
+ {
+ dh.selectDataSet(g);
+
+ if (bSurface)
+ {
+ // Special loop for surface calculation, where a separate neighbor
+ // search is done for each position in the selection, and the
+ // nearest position from each surface group is tracked.
+ std::vector<real> &surfaceDist2 = frameData.surfaceDist2_;
+ for (int i = 0; i < sel[g].posCount(); ++i)
+ {
+ std::fill(surfaceDist2.begin(), surfaceDist2.end(),
+ std::numeric_limits<real>::max());
+ AnalysisNeighborhoodPairSearch pairSearch =
+ nbsearch.startPairSearch(sel[g].position(i));
+ AnalysisNeighborhoodPair pair;
+ while (pairSearch.findNextPair(&pair))
+ {
+ const real r2 = pair.distance2();
+ const int refId = refSel.position(pair.refIndex()).mappedId();
+ if (r2 < surfaceDist2[refId])
+ {
+ surfaceDist2[refId] = r2;
+ }
+ }
+ // Accumulate the RDF from the distances to the surface.
+ for (size_t i = 0; i < surfaceDist2.size(); ++i)
+ {
+ const real r2 = surfaceDist2[i];
+ // Here, we need to check for rmax, since the value might
+ // be above the cutoff if no points were close to some
+ // surface positions.
+ if (r2 > cut2_ && r2 <= rmax2_)
+ {
+ dh.setPoint(0, std::sqrt(r2));
+ dh.finishPointSet();
+ }
+ }
+ }
+ }
+ else
+ {
+ // Standard neighborhood search over all pairs within the cutoff
+ // for the -surf no case.
+ AnalysisNeighborhoodPairSearch pairSearch = nbsearch.startPairSearch(sel[g]);
+ AnalysisNeighborhoodPair pair;
+ while (pairSearch.findNextPair(&pair))
+ {
+ const real r2 = pair.distance2();
+ if (r2 > cut2_)
+ {
+ // TODO: Consider whether the histogramming could be done with
+ // less overhead (after first measuring the overhead).
+ dh.setPoint(0, std::sqrt(r2));
+ dh.finishPointSet();
+ }
+ }
+ }
+ // Normalization factor for the number density (only used without
+ // -surf, but does not hurt to populate otherwise).
+ nh.setPoint(g + 1, sel[g].posCount() * inverseVolume);
+ }
+ dh.finishFrame();
+ nh.finishFrame();
+}
+
+void
+Rdf::finishAnalysis(int /*nframes*/)
+{
+ // Normalize the averager with the number of reference positions,
+ // from where the normalization propagates to all the output.
+ const real refPosCount = normAve_->average(0, 0);
+ pairCounts_->averager().scaleAll(1.0 / refPosCount);
+ pairCounts_->averager().done();
+
+ // TODO: Consider how these could be exposed to the testing framework
+ // through the dataset registration mechanism.
+ AverageHistogramPointer finalRdf
+ = pairCounts_->averager().resampleDoubleBinWidth(true);
+
+ if (bNormalize_)
+ {
+ // Normalize by the volume of the bins (volume of sphere segments or
+ // length of circle segments).
+ std::vector<real> invBinVolume;
+ const int nbin = finalRdf->settings().binCount();
+ invBinVolume.resize(nbin);
+ real prevSphereVolume = 0.0;
+ for (int i = 0; i < nbin; ++i)
+ {
+ const real r = (i + 0.5)*binwidth_;
+ real sphereVolume;
+ if (bXY_)
+ {
+ sphereVolume = M_PI*r*r;
+ }
+ else
+ {
+ sphereVolume = (4.0/3.0)*M_PI*r*r*r;
+ }
+ const real binVolume = sphereVolume - prevSphereVolume;
+ invBinVolume[i] = 1.0 / binVolume;
+ prevSphereVolume = sphereVolume;
+ }
+ finalRdf->scaleAllByVector(&invBinVolume[0]);
+
+ // Normalize by particle density.
+ for (size_t g = 0; g < sel_.size(); ++g)
+ {
+ finalRdf->scaleSingle(g, 1.0 / normAve_->average(0, g + 1));
+ }
+ }
+ else
+ {
+ // With -nonorm, just scale with bin width to make the integral of the
+ // curve (instead of raw bin sum) represent the pair count.
+ finalRdf->scaleAll(1.0 / binwidth_);
+ }
+ finalRdf->done();
+
+ // TODO: Consider if some of this should be done in writeOutput().
+ {
+ AnalysisDataPlotModulePointer plotm(
+ new AnalysisDataPlotModule(plotSettings_));
+ plotm->setFileName(fnRdf_);
+ plotm->setTitle("Radial distribution");
+ plotm->setSubtitle(formatString("reference %s", refSel_.name()));
+ plotm->setXLabel("r (nm)");
+ plotm->setYLabel("g(r)");
+ for (size_t i = 0; i < sel_.size(); ++i)
+ {
+ plotm->appendLegend(sel_[i].name());
+ }
+ finalRdf->addModule(plotm);
+ }
+
+ if (!fnCumulative_.empty())
+ {
+ AverageHistogramPointer cumulativeRdf
+ = pairCounts_->averager().resampleDoubleBinWidth(false);
+ cumulativeRdf->makeCumulative();
+ cumulativeRdf->done();
+
+ AnalysisDataPlotModulePointer plotm(
+ new AnalysisDataPlotModule(plotSettings_));
+ plotm->setFileName(fnCumulative_);
+ plotm->setTitle("Cumulative Number RDF");
+ plotm->setSubtitle(formatString("reference %s", refSel_.name()));
+ plotm->setXLabel("r (nm)");
+ plotm->setYLabel("number");
+ for (size_t i = 0; i < sel_.size(); ++i)
+ {
+ plotm->appendLegend(sel_[i].name());
+ }
+ cumulativeRdf->addModule(plotm);
+ }
+}
+
+void
+Rdf::writeOutput()
+{
+}
+
+//! \}
+
+} // namespace
+
+const char RdfInfo::name[] = "rdf";
+const char RdfInfo::shortDescription[] =
+ "Calculate radial distribution functions";
+
+TrajectoryAnalysisModulePointer RdfInfo::create()
+{
+ return TrajectoryAnalysisModulePointer(new Rdf);
+}
+
+} // namespace analysismodules
+
+} // namespace gmx
--- /dev/null
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 2014, by the GROMACS development team, led by
+ * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+ * and including many others, as listed in the AUTHORS file in the
+ * top-level source directory and at http://www.gromacs.org.
+ *
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
+ * of the License, or (at your option) any later version.
+ *
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+ *
+ * If you want to redistribute modifications to GROMACS, please
+ * consider that scientific software is very special. Version
+ * control is crucial - bugs must be traceable. We will be happy to
+ * consider code for inclusion in the official distribution, but
+ * derived work must not be called official GROMACS. Details are found
+ * in the README & COPYING files - if they are missing, get the
+ * official version at http://www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the research papers on the package. Check out http://www.gromacs.org.
+ */
+/*! \internal \file
+ * \brief
+ * Declares trajectory analysis module for RDF calculations.
+ *
+ * \author Teemu Murtola <teemu.murtola@gmail.com>
+ * \ingroup module_trajectoryanalysis
+ */
+#ifndef GMX_TRAJECTORYANALYSIS_MODULES_RDF_H
+#define GMX_TRAJECTORYANALYSIS_MODULES_RDF_H
+
+#include "gromacs/trajectoryanalysis/analysismodule.h"
+
+namespace gmx
+{
+
+namespace analysismodules
+{
+
+class RdfInfo
+{
+ public:
+ static const char name[];
+ static const char shortDescription[];
+ static TrajectoryAnalysisModulePointer create();
+};
+
+} // namespace analysismodules
+
+} // namespace gmx
+
+#endif
distance.cpp
freevolume.cpp
pairdist.cpp
+ rdf.cpp
sasa.cpp
select.cpp
surfacearea.cpp
--- /dev/null
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 2014, by the GROMACS development team, led by
+ * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+ * and including many others, as listed in the AUTHORS file in the
+ * top-level source directory and at http://www.gromacs.org.
+ *
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
+ * of the License, or (at your option) any later version.
+ *
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+ *
+ * If you want to redistribute modifications to GROMACS, please
+ * consider that scientific software is very special. Version
+ * control is crucial - bugs must be traceable. We will be happy to
+ * consider code for inclusion in the official distribution, but
+ * derived work must not be called official GROMACS. Details are found
+ * in the README & COPYING files - if they are missing, get the
+ * official version at http://www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the research papers on the package. Check out http://www.gromacs.org.
+ */
+/*! \internal \file
+ * \brief
+ * Tests for functionality of the "rdf" trajectory analysis module.
+ *
+ * These tests are essentially regression tests for the actual RDF calculation
+ * from very small configurations. Exclusions are not tested (since the input
+ * does not contain any), nor is the effect of -cut of -rmax.
+ * At the moment, they do not test the final normalization, but only the pair
+ * counts calculated for each frame. Tests for the final normalization should
+ * be added once related TODOs in the implementation/framework have been
+ * resolved (currently, the test framework does not see the final output data).
+ *
+ * \author Teemu Murtola <teemu.murtola@gmail.com>
+ * \ingroup module_trajectoryanalysis
+ */
+#include "gmxpre.h"
+
+#include "gromacs/trajectoryanalysis/modules/rdf.h"
+
+#include <gtest/gtest.h>
+
+#include "testutils/cmdlinetest.h"
+#include "testutils/testasserts.h"
+
+#include "moduletest.h"
+
+namespace
+{
+
+using gmx::test::CommandLine;
+
+/********************************************************************
+ * Tests for gmx::analysismodules::Rdf.
+ */
+
+//! Test fixture for the `rdf` analysis module.
+typedef gmx::test::TrajectoryAnalysisModuleTestFixture<gmx::analysismodules::RdfInfo>
+ RdfModuleTest;
+
+TEST_F(RdfModuleTest, BasicTest)
+{
+ const char *const cmdline[] = {
+ "rdf",
+ "-bin", "0.05",
+ "-ref", "name OW",
+ "-sel", "name OW", "not name OW"
+ };
+ setTopology("spc216.gro");
+ setOutputFileNoTest("-o", "xvg");
+ excludeDataset("pairdist");
+ runTest(CommandLine(cmdline));
+}
+
+TEST_F(RdfModuleTest, CalculatesSurf)
+{
+ const char *const cmdline[] = {
+ "rdf",
+ "-bin", "0.05", "-surf", "res",
+ "-ref", "within 0.5 of (resnr 1 and name OW)",
+ "-sel", "name OW", "not name OW"
+ };
+ setTopology("spc216.gro");
+ setOutputFileNoTest("-o", "xvg");
+ excludeDataset("pairdist");
+ runTest(CommandLine(cmdline));
+}
+
+TEST_F(RdfModuleTest, CalculatesXY)
+{
+ const char *const cmdline[] = {
+ "rdf",
+ "-bin", "0.05", "-xy",
+ "-ref", "name OW",
+ "-sel", "name OW", "not name OW"
+ };
+ setTopology("spc216.gro");
+ setOutputFileNoTest("-o", "xvg");
+ excludeDataset("pairdist");
+ // TODO: Consider if it is possible to get a more reproducible result
+ // and/or a stricter tolerance (e.g., by checking that the sum of
+ // neighboring values still stays constant).
+ setDatasetTolerance("paircount", gmx::test::absoluteTolerance(2.5));
+ runTest(CommandLine(cmdline));
+}
+
+} // namespace
--- /dev/null
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--- /dev/null
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+ <Real Name="Value">352</Real>
+ </DataValue>
+ </DataValues>
+ </DataFrame>
+ </AnalysisData>
+ </OutputData>
+</ReferenceData>
--- /dev/null
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+<ReferenceData>
+ <String Name="CommandLine">rdf -bin 0.05 -xy -ref 'name OW' -sel 'name OW' 'not name OW'</String>
+ <OutputData Name="Data">
+ <AnalysisData Name="norm">
+ <DataFrame Name="Frame0">
+ <Real Name="X">0</Real>
+ <DataValues>
+ <Int Name="Count">3</Int>
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+ </DataValue>
+ <DataValue>
+ <Real Name="Value">124.59379238177897</Real>
+ </DataValue>
+ </DataValues>
+ </DataFrame>
+ </AnalysisData>
+ <AnalysisData Name="paircount">
+ <DataFrame Name="Frame0">
+ <Real Name="X">0</Real>
+ <DataValues>
+ <Int Name="Count">37</Int>
+ <Int Name="DataSet">0</Int>
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+ </DataValue>
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+ </DataValue>
+ </DataValues>
+ <DataValues>
+ <Int Name="Count">37</Int>
+ <Int Name="DataSet">1</Int>
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+ <Real Name="Value">64</Real>
+ </DataValue>
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+ </DataValue>
+ <DataValue>
+ <Real Name="Value">288</Real>
+ </DataValue>
+ <DataValue>
+ <Real Name="Value">567</Real>
+ </DataValue>
+ <DataValue>
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+ </DataValue>
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+ </DataValue>
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+ </DataValue>
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+ </DataValue>
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+ </DataValue>
+ <DataValue>
+ <Real Name="Value">897</Real>
+ </DataValue>
+ <DataValue>
+ <Real Name="Value">1094</Real>
+ </DataValue>
+ <DataValue>
+ <Real Name="Value">1236</Real>
+ </DataValue>
+ <DataValue>
+ <Real Name="Value">1394</Real>
+ </DataValue>
+ <DataValue>
+ <Real Name="Value">1504</Real>
+ </DataValue>
+ <DataValue>
+ <Real Name="Value">1568</Real>
+ </DataValue>
+ <DataValue>
+ <Real Name="Value">1691</Real>
+ </DataValue>
+ <DataValue>
+ <Real Name="Value">1770</Real>
+ </DataValue>
+ <DataValue>
+ <Real Name="Value">1827</Real>
+ </DataValue>
+ <DataValue>
+ <Real Name="Value">1907</Real>
+ </DataValue>
+ <DataValue>
+ <Real Name="Value">2001</Real>
+ </DataValue>
+ <DataValue>
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+ </DataValue>
+ <DataValue>
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+ </DataValue>
+ <DataValue>
+ <Real Name="Value">2367</Real>
+ </DataValue>
+ <DataValue>
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+ </DataValue>
+ <DataValue>
+ <Real Name="Value">2546</Real>
+ </DataValue>
+ <DataValue>
+ <Real Name="Value">2731</Real>
+ </DataValue>
+ <DataValue>
+ <Real Name="Value">2909</Real>
+ </DataValue>
+ <DataValue>
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+ </DataValue>
+ <DataValue>
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+ </DataValue>
+ <DataValue>
+ <Real Name="Value">3038</Real>
+ </DataValue>
+ <DataValue>
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+ </DataValue>
+ <DataValue>
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+ </DataValue>
+ <DataValue>
+ <Real Name="Value">3507</Real>
+ </DataValue>
+ <DataValue>
+ <Real Name="Value">3404</Real>
+ </DataValue>
+ <DataValue>
+ <Real Name="Value">3612</Real>
+ </DataValue>
+ <DataValue>
+ <Real Name="Value">3945</Real>
+ </DataValue>
+ <DataValue>
+ <Real Name="Value">3388</Real>
+ </DataValue>
+ </DataValues>
+ </DataFrame>
+ </AnalysisData>
+ </OutputData>
+</ReferenceData>
using gmx::test::CommandLine;
/********************************************************************
- * Tests for gmx::analysismodules::Sas.
+ * Tests for gmx::analysismodules::Sasa.
*/
-//! Test fixture for the select analysis module.
+//! Test fixture for the `sasa` analysis module.
typedef gmx::test::TrajectoryAnalysisModuleTestFixture<gmx::analysismodules::SasaInfo>
SasaModuleTest;
--- /dev/null
+216H2O,WATJP01,SPC216,SPC-MODEL,300K,BOX(M)=1.86206NM,WFVG,MAR. 1984
+ 648
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+ 1SOL HW1 2 .137 .626 .150
+ 1SOL HW2 3 .231 .589 .021
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+ 3SOL OW 7 .019 .368 .647
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g_potential
g_principal
g_rama
- g_rdf
g_rms
g_rmsdist
g_rmsf
"Calculate principal axes of inertia for a group of atoms");
registerModule(manager, &gmx_rama, "rama",
"Compute Ramachandran plots");
- registerModule(manager, &gmx_rdf, "rdf",
- "Calculate radial distribution functions");
registerModule(manager, &gmx_rms, "rms",
"Calculate RMSDs with a reference structure and RMSD matrices");
registerModule(manager, &gmx_rmsdist, "rmsdist",
biod.pnpi.spb.ru / alexxy / gromacs.git / commitdiff