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33 * GROwing Monsters And Cloning Shrimps
49 #include "gmx_fatal.h"
61 static char pulldim[STRLEN];
63 static void string2dvec(char buf[], dvec nums)
65 if (sscanf(buf,"%lf%lf%lf",&nums[0],&nums[1],&nums[2]) != 3)
66 gmx_fatal(FARGS,"Expected three numbers at input line %s",buf);
69 static void init_pullgrp(t_pullgrp *pg,char *wbuf,
70 gmx_bool bRef,int eGeom,char *s_vec)
77 while (sscanf(wbuf,"%lf %n",&d,&n) == 1) {
78 if (pg->nweight % 100 == 0) {
79 srenew(pg->weight,pg->nweight+100);
81 pg->weight[pg->nweight++] = d;
85 if (eGeom == epullgDIST) {
88 string2dvec(s_vec,vec);
89 if (eGeom == epullgDIR || eGeom == epullgCYL ||
90 (eGeom == epullgPOS && dnorm(vec) != 0))
91 /* Normalize the direction vector */
92 dsvmul(1/dnorm(vec),vec,vec);
99 char **read_pullparams(int *ninp_p,t_inpfile **inp_p,
100 t_pull *pull,gmx_bool *bStart,
103 int ninp,nerror=0,i,nchar,ndim,nscan,m;
107 char dummy[STRLEN],buf[STRLEN],init[STRLEN];
108 const char *init_def1="0.0",*init_def3="0.0 0.0 0.0";
109 char wbuf[STRLEN],VecTemp[STRLEN];
117 /* read pull parameters */
118 CTYPE("Pull geometry: distance, direction, cylinder or position");
119 EETYPE("pull_geometry", pull->eGeom, epullg_names);
120 CTYPE("Select components for the pull vector. default: Y Y Y");
121 STYPE("pull_dim", pulldim, "Y Y Y");
122 CTYPE("Cylinder radius for dynamic reaction force groups (nm)");
123 RTYPE("pull_r1", pull->cyl_r1, 1.0);
124 CTYPE("Switch from r1 to r0 in case of dynamic reaction force");
125 RTYPE("pull_r0", pull->cyl_r0, 1.5);
126 RTYPE("pull_constr_tol", pull->constr_tol, 1E-6);
127 EETYPE("pull_start", *bStart, yesno_names);
128 ITYPE("pull_nstxout", pull->nstxout, 10);
129 ITYPE("pull_nstfout", pull->nstfout, 1);
130 CTYPE("Number of pull groups");
131 ITYPE("pull_ngroups", pull->ngrp,1);
133 if (pull->cyl_r1 > pull->cyl_r0) {
134 warning_error(wi,"pull_r1 > pull_r0");
137 if (pull->ngrp < 1) {
138 gmx_fatal(FARGS,"pull_ngroups should be >= 1");
141 snew(pull->grp,pull->ngrp+1);
143 if (pull->eGeom == epullgPOS) {
149 /* pull group options */
150 CTYPE("Group name, weight (default all 1), vector, init, rate (nm/ps), kJ/(mol*nm^2)");
151 /* Read the pull groups */
152 snew(grpbuf,pull->ngrp+1);
153 for(i=0; i<pull->ngrp+1; i++) {
154 pgrp = &pull->grp[i];
155 snew(grpbuf[i],STRLEN);
156 sprintf(buf,"pull_group%d",i);
157 STYPE(buf, grpbuf[i], "");
158 sprintf(buf,"pull_weights%d",i);
159 STYPE(buf, wbuf, "");
160 sprintf(buf,"pull_pbcatom%d",i);
161 ITYPE(buf, pgrp->pbcatom, 0);
163 sprintf(buf,"pull_vec%d",i);
164 STYPE(buf, VecTemp, "0.0 0.0 0.0");
165 sprintf(buf,"pull_init%d",i);
166 STYPE(buf, init, ndim==1 ? init_def1 : init_def3);
167 nscan = sscanf(init,"%lf %lf %lf",&vec[0],&vec[1],&vec[2]);
169 fprintf(stderr,"ERROR: %s should have %d components\n",buf,ndim);
172 for(m=0; m<DIM; m++) {
173 pgrp->init[m] = (m<ndim ? vec[m] : 0.0);
175 sprintf(buf,"pull_rate%d",i);
176 RTYPE(buf, pgrp->rate, 0.0);
177 sprintf(buf,"pull_k%d",i);
178 RTYPE(buf, pgrp->k, 0.0);
179 sprintf(buf,"pull_kB%d",i);
180 RTYPE(buf, pgrp->kB, pgrp->k);
183 /* Initialize the pull group */
184 init_pullgrp(pgrp,wbuf,i==0,pull->eGeom,VecTemp);
193 void make_pull_groups(t_pull *pull,char **pgnames,t_blocka *grps,char **gnames)
195 int d,nchar,g,ig=-1,i;
196 char *ptr,pulldim1[STRLEN];
201 for(d=0; d<DIM; d++) {
202 if (sscanf(ptr,"%s%n",pulldim1,&nchar) != 1)
203 gmx_fatal(FARGS,"Less than 3 pull dimensions given in pull_dim: '%s'",
206 if (gmx_strncasecmp(pulldim1,"N",1) == 0) {
208 } else if (gmx_strncasecmp(pulldim1,"Y",1) == 0) {
212 gmx_fatal(FARGS,"Please use Y(ES) or N(O) for pull_dim only (not %s)",
218 gmx_fatal(FARGS,"All entries in pull_dim are N");
220 for(g=0; g<pull->ngrp+1; g++) {
221 pgrp = &pull->grp[g];
222 if (g == 0 && strcmp(pgnames[g],"") == 0) {
225 ig = search_string(pgnames[g],grps->nr,gnames);
226 pgrp->nat = grps->index[ig+1] - grps->index[ig];
229 fprintf(stderr,"Pull group %d '%s' has %d atoms\n",
230 g,pgnames[g],pgrp->nat);
231 snew(pgrp->ind,pgrp->nat);
232 for(i=0; i<pgrp->nat; i++)
233 pgrp->ind[i] = grps->a[grps->index[ig]+i];
235 if (pull->eGeom == epullgCYL && g == 0 && pgrp->nweight > 0)
236 gmx_fatal(FARGS,"Weights are not supported for the reference group with cylinder pulling");
237 if (pgrp->nweight > 0 && pgrp->nweight != pgrp->nat)
238 gmx_fatal(FARGS,"Number of weights (%d) for pull group %d '%s' does not match the number of atoms (%d)",
239 pgrp->nweight,g,pgnames[g],pgrp->nat);
241 if (pgrp->nat == 1) {
242 /* No pbc is required for this group */
245 if (pgrp->pbcatom > 0) {
247 } else if (pgrp->pbcatom == 0) {
248 pgrp->pbcatom = pgrp->ind[(pgrp->nat-1)/2];
250 /* Use cosine weighting */
255 if (g > 0 && pull->eGeom != epullgDIST) {
256 for(d=0; d<DIM; d++) {
257 if (pgrp->vec[d] != 0 && pull->dim[d] == 0) {
258 gmx_fatal(FARGS,"ERROR: pull_vec%d has non-zero %c-component while pull_dim in N\n",g,'x'+d);
263 if ((pull->eGeom == epullgDIR || pull->eGeom == epullgCYL) &&
264 g > 0 && norm2(pgrp->vec) == 0)
265 gmx_fatal(FARGS,"pull_vec%d can not be zero with geometry %s",
266 g,EPULLGEOM(pull->eGeom));
267 if ((pull->eGeom == epullgPOS) && pgrp->rate != 0 &&
268 g > 0 && norm2(pgrp->vec) == 0)
269 gmx_fatal(FARGS,"pull_vec%d can not be zero with geometry %s and non-zero rate",
270 g,EPULLGEOM(pull->eGeom));
273 if (pull->eGeom == epullgCYL)
274 gmx_fatal(FARGS,"Absolute reference groups are not supported with geometry %s",EPULLGEOM(pull->eGeom));
276 gmx_fatal(FARGS,"Pull group %d '%s' is empty",g,pgnames[g]);
283 void set_pull_init(t_inputrec *ir,gmx_mtop_t *mtop,rvec *x,matrix box,
284 const output_env_t oenv,gmx_bool bStart)
291 double t_start,tinvrate;
296 /* need to pass in the correct masses if free energy is on*/
299 lambda = ir->fepvals->all_lambda[efptMASS][ir->fepvals->init_fep_state];
301 init_pull(NULL,ir,0,NULL,mtop,NULL,oenv,lambda,FALSE,0);
302 md = init_mdatoms(NULL,mtop,ir->efep);
303 atoms2md(mtop,ir,0,NULL,0,mtop->natoms,md);
305 update_mdatoms(md,ir->fepvals->init_lambda);
308 if (pull->eGeom == epullgPOS)
313 set_pbc(&pbc,ir->ePBC,box);
315 t_start = ir->init_t + ir->init_step*ir->delta_t;
317 pull_calc_coms(NULL,pull,md,&pbc,t_start,x,NULL);
319 fprintf(stderr,"Pull group natoms pbc atom distance at start reference at t=0\n");
320 for(g=0; g<pull->ngrp+1; g++) {
321 pgrp = &pull->grp[g];
322 fprintf(stderr,"%8d %8d %8d ",g,pgrp->nat,pgrp->pbcatom+1);
323 copy_rvec(pgrp->init,init);
324 clear_rvec(pgrp->init);
329 tinvrate = t_start/pgrp->rate;
330 get_pullgrp_distance(pull,&pbc,g,0,dr,dev);
331 for(m=0; m<DIM; m++) {
333 fprintf(stderr," %6.3f",dev[m]);
338 for(m=0; m<DIM; m++) {
340 pgrp->init[m] = init[m] + dev[m]
341 - tinvrate*(pull->eGeom==epullgPOS ? pgrp->vec[m] : 1);
343 pgrp->init[m] = init[m];
345 fprintf(stderr," %6.3f",pgrp->init[m]);
350 fprintf(stderr,"\n");