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42 #include "gromacs/gmxlib/readinp.h"
43 #include "gromacs/gmxpreprocess/readir.h"
44 #include "gromacs/math/vec.h"
45 #include "gromacs/mdlib/mdatoms.h"
46 #include "gromacs/mdtypes/md_enums.h"
47 #include "gromacs/mdtypes/pull-params.h"
48 #include "gromacs/pbcutil/pbc.h"
49 #include "gromacs/pulling/pull.h"
50 #include "gromacs/topology/topology.h"
51 #include "gromacs/utility/cstringutil.h"
52 #include "gromacs/utility/fatalerror.h"
53 #include "gromacs/utility/futil.h"
54 #include "gromacs/utility/smalloc.h"
57 static void string2dvec(const char buf
[], dvec nums
)
61 if (sscanf(buf
, "%lf%lf%lf%lf", &nums
[0], &nums
[1], &nums
[2], &dum
) != 3)
63 gmx_fatal(FARGS
, "Expected three numbers at input line %s", buf
);
67 static void init_pull_group(t_pull_group
*pg
,
74 while (sscanf(wbuf
, "%lf %n", &d
, &n
) == 1)
76 if (pg
->nweight
% 100 == 0)
78 srenew(pg
->weight
, pg
->nweight
+100);
80 pg
->weight
[pg
->nweight
++] = d
;
85 static void process_pull_dim(char *dim_buf
, ivec dim
)
88 char *ptr
, pulldim1
[STRLEN
];
92 for (d
= 0; d
< DIM
; d
++)
94 if (sscanf(ptr
, "%s%n", pulldim1
, &nchar
) != 1)
96 gmx_fatal(FARGS
, "Less than 3 pull dimensions given in pull_dim: '%s'",
100 if (gmx_strncasecmp(pulldim1
, "N", 1) == 0)
104 else if (gmx_strncasecmp(pulldim1
, "Y", 1) == 0)
111 gmx_fatal(FARGS
, "Please use Y(ES) or N(O) for pull_dim only (not %s)",
118 gmx_fatal(FARGS
, "All entries in pull dim are N");
122 static void init_pull_coord(t_pull_coord
*pcrd
,
124 const char *origin_buf
, const char *vec_buf
,
131 if (pcrd
->eType
== epullCONSTRAINT
&& (pcrd
->eGeom
== epullgCYL
||
132 pcrd
->eGeom
== epullgDIRRELATIVE
))
134 gmx_fatal(FARGS
, "Pulling of type %s can not be combined with geometry %s. Consider using pull type %s.",
135 epull_names
[pcrd
->eType
],
136 epullg_names
[pcrd
->eGeom
],
137 epull_names
[epullUMBRELLA
]);
140 process_pull_dim(dim_buf
, pcrd
->dim
);
142 string2dvec(origin_buf
, origin
);
143 if (pcrd
->group
[0] != 0 && dnorm(origin
) > 0)
145 gmx_fatal(FARGS
, "The pull origin can only be set with an absolute reference");
148 /* Check and set the pull vector */
150 if (pcrd
->eGeom
== epullgDIST
)
154 sprintf(buf
, "The initial pull distance is negative with geometry %s, while a distance can not be negative. Use geometry %s instead.",
155 EPULLGEOM(pcrd
->eGeom
), EPULLGEOM(epullgDIR
));
156 warning_error(wi
, buf
);
158 /* TODO: With a positive init but a negative rate things could still
159 * go wrong, but it might be fine if you don't pull too far.
160 * We should give a warning or note when there is only one pull dim
161 * active, since that is usually the problematic case when you should
162 * be using direction. We will do this later, since an already planned
163 * generalization of the pull code makes pull dim available here.
166 else if (pcrd
->eGeom
!= epullgDIRRELATIVE
)
168 string2dvec(vec_buf
, vec
);
169 if (dnorm2(vec
) == 0)
171 gmx_fatal(FARGS
, "With pull geometry %s the pull vector can not be 0,0,0",
172 epullg_names
[pcrd
->eGeom
]);
174 if (pcrd
->eGeom
== epullgDIR
|| pcrd
->eGeom
== epullgCYL
)
176 /* Normalize the direction vector */
177 dsvmul(1/dnorm(vec
), vec
, vec
);
180 for (m
= 0; m
< DIM
; m
++)
182 pcrd
->origin
[m
] = origin
[m
];
183 pcrd
->vec
[m
] = vec
[m
];
187 char **read_pullparams(int *ninp_p
, t_inpfile
**inp_p
,
191 int ninp
, i
, nscan
, idum
;
195 char buf
[STRLEN
], groups
[STRLEN
], dim_buf
[STRLEN
];
196 char wbuf
[STRLEN
], origin_buf
[STRLEN
], vec_buf
[STRLEN
];
204 /* read pull parameters */
205 CTYPE("Cylinder radius for dynamic reaction force groups (nm)");
206 RTYPE("pull-cylinder-r", pull
->cylinder_r
, 1.5);
207 RTYPE("pull-constr-tol", pull
->constr_tol
, 1E-6);
208 EETYPE("pull-print-com1", pull
->bPrintCOM1
, yesno_names
);
209 EETYPE("pull-print-com2", pull
->bPrintCOM2
, yesno_names
);
210 EETYPE("pull-print-ref-value", pull
->bPrintRefValue
, yesno_names
);
211 EETYPE("pull-print-components", pull
->bPrintComp
, yesno_names
);
212 ITYPE("pull-nstxout", pull
->nstxout
, 50);
213 ITYPE("pull-nstfout", pull
->nstfout
, 50);
214 CTYPE("Number of pull groups");
215 ITYPE("pull-ngroups", pull
->ngroup
, 1);
216 CTYPE("Number of pull coordinates");
217 ITYPE("pull-ncoords", pull
->ncoord
, 1);
219 if (pull
->ngroup
< 1)
221 gmx_fatal(FARGS
, "pull-ngroups should be >= 1");
223 /* We always add an absolute reference group (index 0), even if not used */
226 if (pull
->ncoord
< 1)
228 gmx_fatal(FARGS
, "pull-ncoords should be >= 1");
231 snew(pull
->group
, pull
->ngroup
);
233 snew(pull
->coord
, pull
->ncoord
);
235 /* pull group options */
236 CTYPE("Group name, weight (default all 1), vector, init, rate (nm/ps), kJ/(mol*nm^2)");
238 /* Read the pull groups */
239 snew(grpbuf
, pull
->ngroup
);
240 /* Group 0 is the absolute reference, we don't read anything for 0 */
241 for (i
= 1; i
< pull
->ngroup
; i
++)
243 pgrp
= &pull
->group
[i
];
244 snew(grpbuf
[i
], STRLEN
);
245 sprintf(buf
, "pull-group%d-name", i
);
246 STYPE(buf
, grpbuf
[i
], "");
247 sprintf(buf
, "pull-group%d-weights", i
);
248 STYPE(buf
, wbuf
, "");
249 sprintf(buf
, "pull-group%d-pbcatom", i
);
250 ITYPE(buf
, pgrp
->pbcatom
, 0);
252 /* Initialize the pull group */
253 init_pull_group(pgrp
, wbuf
);
256 /* Read the pull coordinates */
257 for (i
= 1; i
< pull
->ncoord
+ 1; i
++)
259 pcrd
= &pull
->coord
[i
-1];
260 sprintf(buf
, "pull-coord%d-type", i
);
261 EETYPE(buf
, pcrd
->eType
, epull_names
);
262 sprintf(buf
, "pull-coord%d-geometry", i
);
263 EETYPE(buf
, pcrd
->eGeom
, epullg_names
);
264 sprintf(buf
, "pull-coord%d-groups", i
);
265 STYPE(buf
, groups
, "");
267 pcrd
->ngroup
= (pcrd
->eGeom
== epullgDIRRELATIVE
? 4 : 2);
269 nscan
= sscanf(groups
, "%d %d %d %d %d", &pcrd
->group
[0], &pcrd
->group
[1], &pcrd
->group
[2], &pcrd
->group
[3], &idum
);
270 if (nscan
!= pcrd
->ngroup
)
272 sprintf(wbuf
, "%s should contain %d pull group indices with geometry %s",
273 buf
, pcrd
->ngroup
, epullg_names
[pcrd
->eGeom
]);
274 set_warning_line(wi
, NULL
, -1);
275 warning_error(wi
, wbuf
);
278 sprintf(buf
, "pull-coord%d-dim", i
);
279 STYPE(buf
, dim_buf
, "Y Y Y");
280 sprintf(buf
, "pull-coord%d-origin", i
);
281 STYPE(buf
, origin_buf
, "0.0 0.0 0.0");
282 sprintf(buf
, "pull-coord%d-vec", i
);
283 STYPE(buf
, vec_buf
, "0.0 0.0 0.0");
284 sprintf(buf
, "pull-coord%d-start", i
);
285 EETYPE(buf
, pcrd
->bStart
, yesno_names
);
286 sprintf(buf
, "pull-coord%d-init", i
);
287 RTYPE(buf
, pcrd
->init
, 0.0);
288 sprintf(buf
, "pull-coord%d-rate", i
);
289 RTYPE(buf
, pcrd
->rate
, 0.0);
290 sprintf(buf
, "pull-coord%d-k", i
);
291 RTYPE(buf
, pcrd
->k
, 0.0);
292 sprintf(buf
, "pull-coord%d-kB", i
);
293 RTYPE(buf
, pcrd
->kB
, pcrd
->k
);
295 /* Initialize the pull coordinate */
296 init_pull_coord(pcrd
, dim_buf
, origin_buf
, vec_buf
, wi
);
305 void make_pull_groups(pull_params_t
*pull
,
307 const t_blocka
*grps
, char **gnames
)
312 /* Absolute reference group (might not be used) is special */
313 pgrp
= &pull
->group
[0];
317 for (g
= 1; g
< pull
->ngroup
; g
++)
319 pgrp
= &pull
->group
[g
];
321 if (strcmp(pgnames
[g
], "") == 0)
323 gmx_fatal(FARGS
, "Pull option pull_group%d required by grompp has not been set.", g
);
326 ig
= search_string(pgnames
[g
], grps
->nr
, gnames
);
327 pgrp
->nat
= grps
->index
[ig
+1] - grps
->index
[ig
];
329 fprintf(stderr
, "Pull group %d '%s' has %d atoms\n",
330 g
, pgnames
[g
], pgrp
->nat
);
334 gmx_fatal(FARGS
, "Pull group %d '%s' is empty", g
, pgnames
[g
]);
337 snew(pgrp
->ind
, pgrp
->nat
);
338 for (i
= 0; i
< pgrp
->nat
; i
++)
340 pgrp
->ind
[i
] = grps
->a
[grps
->index
[ig
]+i
];
343 if (pgrp
->nweight
> 0 && pgrp
->nweight
!= pgrp
->nat
)
345 gmx_fatal(FARGS
, "Number of weights (%d) for pull group %d '%s' does not match the number of atoms (%d)",
346 pgrp
->nweight
, g
, pgnames
[g
], pgrp
->nat
);
351 /* No pbc is required for this group */
356 if (pgrp
->pbcatom
> 0)
360 else if (pgrp
->pbcatom
== 0)
362 pgrp
->pbcatom
= pgrp
->ind
[(pgrp
->nat
-1)/2];
366 /* Use cosine weighting */
373 void make_pull_coords(pull_params_t
*pull
)
378 for (c
= 0; c
< pull
->ncoord
; c
++)
380 pcrd
= &pull
->coord
[c
];
382 if (pcrd
->group
[0] < 0 || pcrd
->group
[0] >= pull
->ngroup
||
383 pcrd
->group
[1] < 0 || pcrd
->group
[1] >= pull
->ngroup
)
385 gmx_fatal(FARGS
, "Pull group index in pull-coord%d-groups out of range, should be between %d and %d", c
+1, 0, pull
->ngroup
+1);
388 if (pcrd
->group
[0] == pcrd
->group
[1])
390 gmx_fatal(FARGS
, "Identical pull group indices in pull-coord%d-groups", c
+1);
393 if (pcrd
->eGeom
== epullgCYL
)
395 if (pull
->group
[pcrd
->group
[0]].nweight
> 0)
397 gmx_fatal(FARGS
, "Weights are not supported for the reference group with cylinder pulling");
401 if (pcrd
->eGeom
!= epullgDIST
)
403 for (d
= 0; d
< DIM
; d
++)
405 if (pcrd
->vec
[d
] != 0 && pcrd
->dim
[d
] == 0)
407 gmx_fatal(FARGS
, "ERROR: pull-group%d-vec has non-zero %c-component while pull_dim for the %c-dimension is N\n", c
+1, 'x'+d
, 'x'+d
);
412 if ((pcrd
->eGeom
== epullgDIR
|| pcrd
->eGeom
== epullgCYL
) &&
413 norm2(pcrd
->vec
) == 0)
415 gmx_fatal(FARGS
, "pull-group%d-vec can not be zero with geometry %s",
416 c
+1, EPULLGEOM(pcrd
->eGeom
));
421 void set_pull_init(t_inputrec
*ir
, gmx_mtop_t
*mtop
, rvec
*x
, matrix box
, real lambda
,
422 const gmx_output_env_t
*oenv
)
425 struct pull_t
*pull_work
;
432 pull_work
= init_pull(NULL
, pull
, ir
, 0, NULL
, mtop
, NULL
, oenv
, lambda
, FALSE
, 0);
433 md
= init_mdatoms(NULL
, mtop
, ir
->efep
);
434 atoms2md(mtop
, ir
, 0, NULL
, mtop
->natoms
, md
);
437 update_mdatoms(md
, lambda
);
440 set_pbc(&pbc
, ir
->ePBC
, box
);
442 t_start
= ir
->init_t
+ ir
->init_step
*ir
->delta_t
;
444 pull_calc_coms(NULL
, pull_work
, md
, &pbc
, t_start
, x
, NULL
);
446 fprintf(stderr
, "Pull group natoms pbc atom distance at start reference at t=0\n");
447 for (c
= 0; c
< pull
->ncoord
; c
++)
450 t_pull_group
*pgrp0
, *pgrp1
;
454 pcrd
= &pull
->coord
[c
];
456 pgrp0
= &pull
->group
[pcrd
->group
[0]];
457 pgrp1
= &pull
->group
[pcrd
->group
[1]];
458 fprintf(stderr
, "%8d %8d %8d\n",
459 pcrd
->group
[0], pgrp0
->nat
, pgrp0
->pbcatom
+1);
460 fprintf(stderr
, "%8d %8d %8d ",
461 pcrd
->group
[1], pgrp1
->nat
, pgrp1
->pbcatom
+1);
469 get_pull_coord_value(pull_work
, c
, &pbc
, &value
);
470 fprintf(stderr
, " %10.3f nm", value
);
474 pcrd
->init
= value
+ init
;
476 fprintf(stderr
, " %10.3f nm\n", pcrd
->init
);
479 finish_pull(pull_work
);