/*
- * This source code is part of
- *
- * G R O M A C S
- *
- * GROningen MAchine for Chemical Simulations
- *
- * Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
+ * 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,
- * check out http://www.gromacs.org for more information.
-
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
+ * 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.
- *
- * If you want to redistribute modifications, 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 www.gromacs.org.
- *
+ *
+ * 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 papers on the package - you can find them in the top README file.
- *
- * For more info, check our website at http://www.gromacs.org
- *
- * And Hey:
- * GROwing Monsters And Cloning Shrimps
+ * the research papers on the package. Check out http://www.gromacs.org.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
-
-#include "vec.h"
-#include "smalloc.h"
-#include "readir.h"
-#include "names.h"
-#include "futil.h"
-#include "trnio.h"
-#include "txtdump.h"
+#include "gmxpre.h"
+
+#include "gromacs/fileio/trnio.h"
+#include "gromacs/gmxpreprocess/readir.h"
+#include "gromacs/legacyheaders/names.h"
+#include "gromacs/legacyheaders/txtdump.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/futil.h"
+#include "gromacs/utility/smalloc.h"
static char *RotStr = {"Enforced rotation:"};
static void string2dvec(char buf[], dvec nums)
{
- if (sscanf(buf,"%lf%lf%lf",&nums[0],&nums[1],&nums[2]) != 3)
- gmx_fatal(FARGS,"Expected three numbers at input line %s",buf);
+ if (sscanf(buf, "%lf%lf%lf", &nums[0], &nums[1], &nums[2]) != 3)
+ {
+ gmx_fatal(FARGS, "Expected three numbers at input line %s", buf);
+ }
}
-extern char **read_rotparams(int *ninp_p,t_inpfile **inp_p,t_rot *rot,
- warninp_t wi)
+extern char **read_rotparams(int *ninp_p, t_inpfile **inp_p, t_rot *rot,
+ warninp_t wi)
{
- int ninp,g,m;
- t_inpfile *inp;
+ int ninp, g, m;
+ t_inpfile *inp;
const char *tmp;
- char **grpbuf;
- char buf[STRLEN];
- char warn_buf[STRLEN];
- dvec vec;
- t_rotgrp *rotg;
+ char **grpbuf;
+ char buf[STRLEN];
+ char warn_buf[STRLEN];
+ dvec vec;
+ t_rotgrp *rotg;
ninp = *ninp_p;
inp = *inp_p;
-
+
/* read rotation parameters */
CTYPE("Output frequency for angle, torque and rotation potential energy for the whole group");
ITYPE("rot_nstrout", rot->nstrout, 100);
CTYPE("Output frequency for per-slab data (angles, torques and slab centers)");
ITYPE("rot_nstsout", rot->nstsout, 1000);
CTYPE("Number of rotation groups");
- ITYPE("rot_ngroups", rot->ngrp,1);
-
+ ITYPE("rot_ngroups", rot->ngrp, 1);
+
if (rot->ngrp < 1)
{
- gmx_fatal(FARGS,"rot_ngroups should be >= 1");
+ gmx_fatal(FARGS, "rot_ngroups should be >= 1");
}
-
- snew(rot->grp,rot->ngrp);
-
+
+ snew(rot->grp, rot->ngrp);
+
/* Read the rotation groups */
- snew(grpbuf,rot->ngrp);
- for(g=0; g<rot->ngrp; g++)
+ snew(grpbuf, rot->ngrp);
+ for (g = 0; g < rot->ngrp; g++)
{
rotg = &rot->grp[g];
- snew(grpbuf[g],STRLEN);
+ snew(grpbuf[g], STRLEN);
CTYPE("Rotation group name");
- sprintf(buf,"rot_group%d",g);
+ sprintf(buf, "rot_group%d", g);
STYPE(buf, grpbuf[g], "");
-
+
CTYPE("Rotation potential. Can be iso, iso-pf, pm, pm-pf, rm, rm-pf, rm2, rm2-pf, flex, flex-t, flex2, flex2-t");
- sprintf(buf,"rot_type%d",g);
+ sprintf(buf, "rot_type%d", g);
ETYPE(buf, rotg->eType, erotg_names);
CTYPE("Use mass-weighting of the rotation group positions");
- sprintf(buf,"rot_massw%d",g);
+ sprintf(buf, "rot_massw%d", g);
ETYPE(buf, rotg->bMassW, yesno_names);
CTYPE("Rotation vector, will get normalized");
- sprintf(buf,"rot_vec%d",g);
+ sprintf(buf, "rot_vec%d", g);
STYPE(buf, s_vec, "1.0 0.0 0.0");
- string2dvec(s_vec,vec);
+ string2dvec(s_vec, vec);
/* Normalize the rotation vector */
if (dnorm(vec) != 0)
{
- dsvmul(1.0/dnorm(vec),vec,vec);
+ dsvmul(1.0/dnorm(vec), vec, vec);
}
else
{
}
fprintf(stderr, "%s Group %d (%s) normalized rot. vector: %f %f %f\n",
RotStr, g, erotg_names[rotg->eType], vec[0], vec[1], vec[2]);
- for(m=0; m<DIM; m++)
+ for (m = 0; m < DIM; m++)
+ {
rotg->vec[m] = vec[m];
-
+ }
+
CTYPE("Pivot point for the potentials iso, pm, rm, and rm2 (nm)");
- sprintf(buf,"rot_pivot%d",g);
+ sprintf(buf, "rot_pivot%d", g);
STYPE(buf, s_vec, "0.0 0.0 0.0");
clear_dvec(vec);
- if ( (rotg->eType==erotgISO) || (rotg->eType==erotgPM) || (rotg->eType==erotgRM) || (rotg->eType==erotgRM2) )
- string2dvec(s_vec,vec);
- for(m=0; m<DIM; m++)
+ if ( (rotg->eType == erotgISO) || (rotg->eType == erotgPM) || (rotg->eType == erotgRM) || (rotg->eType == erotgRM2) )
+ {
+ string2dvec(s_vec, vec);
+ }
+ for (m = 0; m < DIM; m++)
+ {
rotg->pivot[m] = vec[m];
+ }
CTYPE("Rotation rate (degree/ps) and force constant (kJ/(mol*nm^2))");
- sprintf(buf,"rot_rate%d",g);
+ sprintf(buf, "rot_rate%d", g);
RTYPE(buf, rotg->rate, 0.0);
- sprintf(buf,"rot_k%d",g);
+ sprintf(buf, "rot_k%d", g);
RTYPE(buf, rotg->k, 0.0);
if (rotg->k <= 0.0)
{
}
CTYPE("Slab distance for flexible axis rotation (nm)");
- sprintf(buf,"rot_slab_dist%d",g);
+ sprintf(buf, "rot_slab_dist%d", g);
RTYPE(buf, rotg->slab_dist, 1.5);
if (rotg->slab_dist <= 0.0)
{
}
CTYPE("Minimum value of Gaussian function for the force to be evaluated (for flex* potentials)");
- sprintf(buf,"rot_min_gauss%d",g);
+ sprintf(buf, "rot_min_gauss%d", g);
RTYPE(buf, rotg->min_gaussian, 1e-3);
if (rotg->min_gaussian <= 0.0)
{
}
CTYPE("Value of additive constant epsilon' (nm^2) for rm2* and flex2* potentials");
- sprintf(buf, "rot_eps%d",g);
+ sprintf(buf, "rot_eps%d", g);
RTYPE(buf, rotg->eps, 1e-4);
- if ( (rotg->eps <= 0.0) && (rotg->eType==erotgRM2 || rotg->eType==erotgFLEX2) )
+ if ( (rotg->eps <= 0.0) && (rotg->eType == erotgRM2 || rotg->eType == erotgFLEX2) )
{
sprintf(warn_buf, "rot_eps%d <= 0", g);
warning_error(wi, warn_buf);
}
CTYPE("Fitting method to determine angle of rotation group (rmsd, norm, or potential)");
- sprintf(buf,"rot_fit_method%d",g);
+ sprintf(buf, "rot_fit_method%d", g);
ETYPE(buf, rotg->eFittype, erotg_fitnames);
CTYPE("For fit type 'potential', nr. of angles around the reference for which the pot. is evaluated");
- sprintf(buf,"rot_potfit_nsteps%d",g);
+ sprintf(buf, "rot_potfit_nsteps%d", g);
ITYPE(buf, rotg->PotAngle_nstep, 21);
- if ( (rotg->eFittype==erotgFitPOT) && (rotg->PotAngle_nstep < 1) )
+ if ( (rotg->eFittype == erotgFitPOT) && (rotg->PotAngle_nstep < 1) )
{
sprintf(warn_buf, "rot_potfit_nsteps%d < 1", g);
warning_error(wi, warn_buf);
}
CTYPE("For fit type 'potential', distance in degrees between two consecutive angles");
- sprintf(buf,"rot_potfit_step%d",g);
+ sprintf(buf, "rot_potfit_step%d", g);
RTYPE(buf, rotg->PotAngle_step, 0.25);
}
-
+
*ninp_p = ninp;
*inp_p = inp;
-
+
return grpbuf;
}
/* Check whether the box is unchanged */
static void check_box_unchanged(matrix f_box, matrix box, char fn[], warninp_t wi)
{
- int i,ii;
- gmx_bool bSame=TRUE;
- char warn_buf[STRLEN];
-
-
- for (i=0; i<DIM; i++)
- for (ii=0; ii<DIM; ii++)
- if (f_box[i][ii] != box[i][ii])
+ int i, ii;
+ gmx_bool bSame = TRUE;
+ char warn_buf[STRLEN];
+
+
+ for (i = 0; i < DIM; i++)
+ {
+ for (ii = 0; ii < DIM; ii++)
+ {
+ if (f_box[i][ii] != box[i][ii])
+ {
bSame = FALSE;
+ }
+ }
+ }
if (!bSame)
{
sprintf(warn_buf, "%s Box size in reference file %s differs from actual box size!",
RotStr, fn);
warning(wi, warn_buf);
- pr_rvecs(stderr,0,"Your box is:",box ,3);
- pr_rvecs(stderr,0,"Box in file:",f_box,3);
+ pr_rvecs(stderr, 0, "Your box is:", box, 3);
+ pr_rvecs(stderr, 0, "Box in file:", f_box, 3);
}
}
/* Extract the reference positions for the rotation group(s) */
extern void set_reference_positions(
- t_rot *rot, gmx_mtop_t *mtop, rvec *x, matrix box,
+ t_rot *rot, rvec *x, matrix box,
const char *fn, gmx_bool bSet, warninp_t wi)
{
- int g,i,ii;
- t_rotgrp *rotg;
+ int g, i, ii;
+ t_rotgrp *rotg;
t_trnheader header; /* Header information of reference file */
- char base[STRLEN],extension[STRLEN],reffile[STRLEN];
- char *extpos;
- rvec f_box[3]; /* Box from reference file */
+ char base[STRLEN], extension[STRLEN], reffile[STRLEN];
+ char *extpos;
+ rvec f_box[3]; /* Box from reference file */
+
-
/* Base name and extension of the reference file: */
strncpy(base, fn, STRLEN - 1);
- base[STRLEN-1]='\0';
- extpos = strrchr(base, '.');
- strcpy(extension,extpos+1);
+ base[STRLEN-1] = '\0';
+ extpos = strrchr(base, '.');
+ strcpy(extension, extpos+1);
*extpos = '\0';
- for (g=0; g<rot->ngrp; g++)
- {
- rotg = &rot->grp[g];
- fprintf(stderr, "%s group %d has %d reference positions.\n",RotStr,g,rotg->nat);
- snew(rotg->x_ref, rotg->nat);
-
- /* Construct the name for the file containing the reference positions for this group: */
- sprintf(reffile, "%s.%d.%s", base,g,extension);
-
- /* If the base filename for the reference position files was explicitly set by
- * the user, we issue a fatal error if the group file can not be found */
- if (bSet && !gmx_fexist(reffile))
- {
- gmx_fatal(FARGS, "%s The file containing the reference positions was not found.\n"
- "Expected the file '%s' for group %d.\n",
- RotStr, reffile, g);
- }
-
- if (gmx_fexist(reffile))
- {
- fprintf(stderr, " Reading them from %s.\n", reffile);
- read_trnheader(reffile, &header);
- if (rotg->nat != header.natoms)
- gmx_fatal(FARGS,"Number of atoms in file %s (%d) does not match the number of atoms in rotation group (%d)!\n",
- reffile, header.natoms, rotg->nat);
- read_trn(reffile, &header.step, &header.t, &header.lambda, f_box, &header.natoms, rotg->x_ref, NULL, NULL);
-
- /* Check whether the box is unchanged and output a warning if not: */
- check_box_unchanged(f_box,box,reffile,wi);
- }
- else
- {
- fprintf(stderr, " Saving them to %s.\n", reffile);
- for(i=0; i<rotg->nat; i++)
- {
- ii = rotg->ind[i];
- copy_rvec(x[ii], rotg->x_ref[i]);
- }
- write_trn(reffile,g,0.0,0.0,box,rotg->nat,rotg->x_ref,NULL,NULL);
- }
- }
+ for (g = 0; g < rot->ngrp; g++)
+ {
+ rotg = &rot->grp[g];
+ fprintf(stderr, "%s group %d has %d reference positions.\n", RotStr, g, rotg->nat);
+ snew(rotg->x_ref, rotg->nat);
+
+ /* Construct the name for the file containing the reference positions for this group: */
+ sprintf(reffile, "%s.%d.%s", base, g, extension);
+
+ /* If the base filename for the reference position files was explicitly set by
+ * the user, we issue a fatal error if the group file can not be found */
+ if (bSet && !gmx_fexist(reffile))
+ {
+ gmx_fatal(FARGS, "%s The file containing the reference positions was not found.\n"
+ "Expected the file '%s' for group %d.\n",
+ RotStr, reffile, g);
+ }
+
+ if (gmx_fexist(reffile))
+ {
+ fprintf(stderr, " Reading them from %s.\n", reffile);
+ read_trnheader(reffile, &header);
+ if (rotg->nat != header.natoms)
+ {
+ gmx_fatal(FARGS, "Number of atoms in file %s (%d) does not match the number of atoms in rotation group (%d)!\n",
+ reffile, header.natoms, rotg->nat);
+ }
+ read_trn(reffile, &header.step, &header.t, &header.lambda, f_box, &header.natoms, rotg->x_ref, NULL, NULL);
+
+ /* Check whether the box is unchanged and output a warning if not: */
+ check_box_unchanged(f_box, box, reffile, wi);
+ }
+ else
+ {
+ fprintf(stderr, " Saving them to %s.\n", reffile);
+ for (i = 0; i < rotg->nat; i++)
+ {
+ ii = rotg->ind[i];
+ copy_rvec(x[ii], rotg->x_ref[i]);
+ }
+ write_trn(reffile, g, 0.0, 0.0, box, rotg->nat, rotg->x_ref, NULL, NULL);
+ }
+ }
}
-extern void make_rotation_groups(t_rot *rot,char **rotgnames,t_blocka *grps,char **gnames)
+extern void make_rotation_groups(t_rot *rot, char **rotgnames, t_blocka *grps, char **gnames)
{
- int g,ig=-1,i;
+ int g, ig = -1, i;
t_rotgrp *rotg;
-
-
- for (g=0; g<rot->ngrp; g++)
+
+
+ for (g = 0; g < rot->ngrp; g++)
{
- rotg = &rot->grp[g];
- ig = search_string(rotgnames[g],grps->nr,gnames);
+ rotg = &rot->grp[g];
+ ig = search_string(rotgnames[g], grps->nr, gnames);
rotg->nat = grps->index[ig+1] - grps->index[ig];
-
+
if (rotg->nat > 0)
{
- fprintf(stderr,"Rotation group %d '%s' has %d atoms\n",g,rotgnames[g],rotg->nat);
- snew(rotg->ind,rotg->nat);
- for(i=0; i<rotg->nat; i++)
- rotg->ind[i] = grps->a[grps->index[ig]+i];
+ fprintf(stderr, "Rotation group %d '%s' has %d atoms\n", g, rotgnames[g], rotg->nat);
+ snew(rotg->ind, rotg->nat);
+ for (i = 0; i < rotg->nat; i++)
+ {
+ rotg->ind[i] = grps->a[grps->index[ig]+i];
+ }
}
else
- gmx_fatal(FARGS,"Rotation group %d '%s' is empty",g,rotgnames[g]);
+ {
+ gmx_fatal(FARGS, "Rotation group %d '%s' is empty", g, rotgnames[g]);
+ }
}
}
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff