*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013, by the GROMACS development team, led by
+ * 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.
#define MAXPTR 254
#define NOGID 255
-#define MAXLAMBDAS 1024
/* Resource parameters
* Do not change any of these until you read the instruction
* message.
*/
-static char tcgrps[STRLEN], tau_t[STRLEN], ref_t[STRLEN],
- acc[STRLEN], accgrps[STRLEN], freeze[STRLEN], frdim[STRLEN],
- energy[STRLEN], user1[STRLEN], user2[STRLEN], vcm[STRLEN], xtc_grps[STRLEN],
- couple_moltype[STRLEN], orirefitgrp[STRLEN], egptable[STRLEN], egpexcl[STRLEN],
- wall_atomtype[STRLEN], wall_density[STRLEN], deform[STRLEN], QMMM[STRLEN];
-static char fep_lambda[efptNR][STRLEN];
-static char lambda_weights[STRLEN];
-static char **pull_grp;
-static char **rot_grp;
-static char anneal[STRLEN], anneal_npoints[STRLEN],
- anneal_time[STRLEN], anneal_temp[STRLEN];
-static char QMmethod[STRLEN], QMbasis[STRLEN], QMcharge[STRLEN], QMmult[STRLEN],
- bSH[STRLEN], CASorbitals[STRLEN], CASelectrons[STRLEN], SAon[STRLEN],
- SAoff[STRLEN], SAsteps[STRLEN], bTS[STRLEN], bOPT[STRLEN];
-static char efield_x[STRLEN], efield_xt[STRLEN], efield_y[STRLEN],
- efield_yt[STRLEN], efield_z[STRLEN], efield_zt[STRLEN];
+typedef struct t_inputrec_strings
+{
+ char tcgrps[STRLEN], tau_t[STRLEN], ref_t[STRLEN],
+ acc[STRLEN], accgrps[STRLEN], freeze[STRLEN], frdim[STRLEN],
+ energy[STRLEN], user1[STRLEN], user2[STRLEN], vcm[STRLEN], xtc_grps[STRLEN],
+ couple_moltype[STRLEN], orirefitgrp[STRLEN], egptable[STRLEN], egpexcl[STRLEN],
+ wall_atomtype[STRLEN], wall_density[STRLEN], deform[STRLEN], QMMM[STRLEN];
+ char fep_lambda[efptNR][STRLEN];
+ char lambda_weights[STRLEN];
+ char **pull_grp;
+ char **rot_grp;
+ char anneal[STRLEN], anneal_npoints[STRLEN],
+ anneal_time[STRLEN], anneal_temp[STRLEN];
+ char QMmethod[STRLEN], QMbasis[STRLEN], QMcharge[STRLEN], QMmult[STRLEN],
+ bSH[STRLEN], CASorbitals[STRLEN], CASelectrons[STRLEN], SAon[STRLEN],
+ SAoff[STRLEN], SAsteps[STRLEN], bTS[STRLEN], bOPT[STRLEN];
+ char efield_x[STRLEN], efield_xt[STRLEN], efield_y[STRLEN],
+ efield_yt[STRLEN], efield_z[STRLEN], efield_zt[STRLEN];
+
+} gmx_inputrec_strings;
+
+static gmx_inputrec_strings *is = NULL;
+
+void init_inputrec_strings()
+{
+ if (is)
+ {
+ gmx_incons("Attempted to call init_inputrec_strings before calling done_inputrec_strings. Only one inputrec (i.e. .mdp file) can be parsed at a time.");
+ }
+ snew(is, 1);
+}
+
+void done_inputrec_strings()
+{
+ sfree(is);
+ is = NULL;
+}
enum {
egrptpALL, /* All particles have to be a member of a group. */
t_lambda *fep = ir->fepvals;
t_expanded *expand = ir->expandedvals;
+ init_inputrec_strings();
inp = read_inpfile(mdparin, &ninp, wi);
snew(dumstr[0], STRLEN);
CTYPE ("number of steps for center of mass motion removal");
ITYPE ("nstcomm", ir->nstcomm, 100);
CTYPE ("group(s) for center of mass motion removal");
- STYPE ("comm-grps", vcm, NULL);
+ STYPE ("comm-grps", is->vcm, NULL);
CCTYPE ("LANGEVIN DYNAMICS OPTIONS");
CTYPE ("Friction coefficient (amu/ps) and random seed");
RTYPE ("xtc-precision", ir->xtcprec, 1000.0);
CTYPE ("This selects the subset of atoms for the .xtc file. You can");
CTYPE ("select multiple groups. By default all atoms will be written.");
- STYPE ("xtc-grps", xtc_grps, NULL);
+ STYPE ("xtc-grps", is->xtc_grps, NULL);
CTYPE ("Selection of energy groups");
- STYPE ("energygrps", energy, NULL);
+ STYPE ("energygrps", is->energy, NULL);
/* Neighbor searching */
CCTYPE ("NEIGHBORSEARCHING PARAMETERS");
CTYPE ("Extension of the potential lookup tables beyond the cut-off");
RTYPE ("table-extension", ir->tabext, 1.0);
CTYPE ("Separate tables between energy group pairs");
- STYPE ("energygrp-table", egptable, NULL);
+ STYPE ("energygrp-table", is->egptable, NULL);
CTYPE ("Spacing for the PME/PPPM FFT grid");
RTYPE ("fourierspacing", ir->fourier_spacing, 0.12);
CTYPE ("FFT grid size, when a value is 0 fourierspacing will be used");
CTYPE ("Temperature coupling");
EETYPE("tcoupl", ir->etc, etcoupl_names);
ITYPE ("nsttcouple", ir->nsttcouple, -1);
- ITYPE("nh-chain-length", ir->opts.nhchainlength, NHCHAINLENGTH);
+ ITYPE("nh-chain-length", ir->opts.nhchainlength, 10);
EETYPE("print-nose-hoover-chain-variables", ir->bPrintNHChains, yesno_names);
CTYPE ("Groups to couple separately");
- STYPE ("tc-grps", tcgrps, NULL);
+ STYPE ("tc-grps", is->tcgrps, NULL);
CTYPE ("Time constant (ps) and reference temperature (K)");
- STYPE ("tau-t", tau_t, NULL);
- STYPE ("ref-t", ref_t, NULL);
+ STYPE ("tau-t", is->tau_t, NULL);
+ STYPE ("ref-t", is->ref_t, NULL);
CTYPE ("pressure coupling");
EETYPE("pcoupl", ir->epc, epcoupl_names);
EETYPE("pcoupltype", ir->epct, epcoupltype_names);
CCTYPE ("OPTIONS FOR QMMM calculations");
EETYPE("QMMM", ir->bQMMM, yesno_names);
CTYPE ("Groups treated Quantum Mechanically");
- STYPE ("QMMM-grps", QMMM, NULL);
+ STYPE ("QMMM-grps", is->QMMM, NULL);
CTYPE ("QM method");
- STYPE("QMmethod", QMmethod, NULL);
+ STYPE("QMmethod", is->QMmethod, NULL);
CTYPE ("QMMM scheme");
EETYPE("QMMMscheme", ir->QMMMscheme, eQMMMscheme_names);
CTYPE ("QM basisset");
- STYPE("QMbasis", QMbasis, NULL);
+ STYPE("QMbasis", is->QMbasis, NULL);
CTYPE ("QM charge");
- STYPE ("QMcharge", QMcharge, NULL);
+ STYPE ("QMcharge", is->QMcharge, NULL);
CTYPE ("QM multiplicity");
- STYPE ("QMmult", QMmult, NULL);
+ STYPE ("QMmult", is->QMmult, NULL);
CTYPE ("Surface Hopping");
- STYPE ("SH", bSH, NULL);
+ STYPE ("SH", is->bSH, NULL);
CTYPE ("CAS space options");
- STYPE ("CASorbitals", CASorbitals, NULL);
- STYPE ("CASelectrons", CASelectrons, NULL);
- STYPE ("SAon", SAon, NULL);
- STYPE ("SAoff", SAoff, NULL);
- STYPE ("SAsteps", SAsteps, NULL);
+ STYPE ("CASorbitals", is->CASorbitals, NULL);
+ STYPE ("CASelectrons", is->CASelectrons, NULL);
+ STYPE ("SAon", is->SAon, NULL);
+ STYPE ("SAoff", is->SAoff, NULL);
+ STYPE ("SAsteps", is->SAsteps, NULL);
CTYPE ("Scale factor for MM charges");
RTYPE ("MMChargeScaleFactor", ir->scalefactor, 1.0);
CTYPE ("Optimization of QM subsystem");
- STYPE ("bOPT", bOPT, NULL);
- STYPE ("bTS", bTS, NULL);
+ STYPE ("bOPT", is->bOPT, NULL);
+ STYPE ("bTS", is->bTS, NULL);
/* Simulated annealing */
CCTYPE("SIMULATED ANNEALING");
CTYPE ("Type of annealing for each temperature group (no/single/periodic)");
- STYPE ("annealing", anneal, NULL);
+ STYPE ("annealing", is->anneal, NULL);
CTYPE ("Number of time points to use for specifying annealing in each group");
- STYPE ("annealing-npoints", anneal_npoints, NULL);
+ STYPE ("annealing-npoints", is->anneal_npoints, NULL);
CTYPE ("List of times at the annealing points for each group");
- STYPE ("annealing-time", anneal_time, NULL);
+ STYPE ("annealing-time", is->anneal_time, NULL);
CTYPE ("Temp. at each annealing point, for each group.");
- STYPE ("annealing-temp", anneal_temp, NULL);
+ STYPE ("annealing-temp", is->anneal_temp, NULL);
/* Startup run */
CCTYPE ("GENERATE VELOCITIES FOR STARTUP RUN");
/* Energy group exclusions */
CCTYPE ("ENERGY GROUP EXCLUSIONS");
CTYPE ("Pairs of energy groups for which all non-bonded interactions are excluded");
- STYPE ("energygrp-excl", egpexcl, NULL);
+ STYPE ("energygrp-excl", is->egpexcl, NULL);
/* Walls */
CCTYPE ("WALLS");
ITYPE ("nwall", ir->nwall, 0);
EETYPE("wall-type", ir->wall_type, ewt_names);
RTYPE ("wall-r-linpot", ir->wall_r_linpot, -1);
- STYPE ("wall-atomtype", wall_atomtype, NULL);
- STYPE ("wall-density", wall_density, NULL);
+ STYPE ("wall-atomtype", is->wall_atomtype, NULL);
+ STYPE ("wall-density", is->wall_density, NULL);
RTYPE ("wall-ewald-zfac", ir->wall_ewald_zfac, 3);
/* COM pulling */
if (ir->ePull != epullNO)
{
snew(ir->pull, 1);
- pull_grp = read_pullparams(&ninp, &inp, ir->pull, &opts->pull_start, wi);
+ is->pull_grp = read_pullparams(&ninp, &inp, ir->pull, &opts->pull_start, wi);
}
/* Enforced rotation */
if (ir->bRot)
{
snew(ir->rot, 1);
- rot_grp = read_rotparams(&ninp, &inp, ir->rot, wi);
+ is->rot_grp = read_rotparams(&ninp, &inp, ir->rot, wi);
}
/* Refinement */
CTYPE ("Orientation restraints force constant and tau for time averaging");
RTYPE ("orire-fc", ir->orires_fc, 0.0);
RTYPE ("orire-tau", ir->orires_tau, 0.0);
- STYPE ("orire-fitgrp", orirefitgrp, NULL);
+ STYPE ("orire-fitgrp", is->orirefitgrp, NULL);
CTYPE ("Output frequency for trace(SD) and S to energy file");
ITYPE ("nstorireout", ir->nstorireout, 100);
/* free energy variables */
CCTYPE ("Free energy variables");
EETYPE("free-energy", ir->efep, efep_names);
- STYPE ("couple-moltype", couple_moltype, NULL);
+ STYPE ("couple-moltype", is->couple_moltype, NULL);
EETYPE("couple-lambda0", opts->couple_lam0, couple_lam);
EETYPE("couple-lambda1", opts->couple_lam1, couple_lam);
EETYPE("couple-intramol", opts->bCoupleIntra, yesno_names);
ITYPE ("init-lambda-state", fep->init_fep_state, -1);
RTYPE ("delta-lambda", fep->delta_lambda, 0.0);
ITYPE ("nstdhdl", fep->nstdhdl, 50);
- STYPE ("fep-lambdas", fep_lambda[efptFEP], NULL);
- STYPE ("mass-lambdas", fep_lambda[efptMASS], NULL);
- STYPE ("coul-lambdas", fep_lambda[efptCOUL], NULL);
- STYPE ("vdw-lambdas", fep_lambda[efptVDW], NULL);
- STYPE ("bonded-lambdas", fep_lambda[efptBONDED], NULL);
- STYPE ("restraint-lambdas", fep_lambda[efptRESTRAINT], NULL);
- STYPE ("temperature-lambdas", fep_lambda[efptTEMPERATURE], NULL);
+ STYPE ("fep-lambdas", is->fep_lambda[efptFEP], NULL);
+ STYPE ("mass-lambdas", is->fep_lambda[efptMASS], NULL);
+ STYPE ("coul-lambdas", is->fep_lambda[efptCOUL], NULL);
+ STYPE ("vdw-lambdas", is->fep_lambda[efptVDW], NULL);
+ STYPE ("bonded-lambdas", is->fep_lambda[efptBONDED], NULL);
+ STYPE ("restraint-lambdas", is->fep_lambda[efptRESTRAINT], NULL);
+ STYPE ("temperature-lambdas", is->fep_lambda[efptTEMPERATURE], NULL);
ITYPE ("calc-lambda-neighbors", fep->lambda_neighbors, 1);
- STYPE ("init-lambda-weights", lambda_weights, NULL);
+ STYPE ("init-lambda-weights", is->lambda_weights, NULL);
EETYPE("dhdl-print-energy", fep->bPrintEnergy, yesno_names);
RTYPE ("sc-alpha", fep->sc_alpha, 0.0);
ITYPE ("sc-power", fep->sc_power, 1);
/* Non-equilibrium MD stuff */
CCTYPE("Non-equilibrium MD stuff");
- STYPE ("acc-grps", accgrps, NULL);
- STYPE ("accelerate", acc, NULL);
- STYPE ("freezegrps", freeze, NULL);
- STYPE ("freezedim", frdim, NULL);
+ STYPE ("acc-grps", is->accgrps, NULL);
+ STYPE ("accelerate", is->acc, NULL);
+ STYPE ("freezegrps", is->freeze, NULL);
+ STYPE ("freezedim", is->frdim, NULL);
RTYPE ("cos-acceleration", ir->cos_accel, 0);
- STYPE ("deform", deform, NULL);
+ STYPE ("deform", is->deform, NULL);
/* simulated tempering variables */
CCTYPE("simulated tempering variables");
CCTYPE("Electric fields");
CTYPE ("Format is number of terms (int) and for all terms an amplitude (real)");
CTYPE ("and a phase angle (real)");
- STYPE ("E-x", efield_x, NULL);
- STYPE ("E-xt", efield_xt, NULL);
- STYPE ("E-y", efield_y, NULL);
- STYPE ("E-yt", efield_yt, NULL);
- STYPE ("E-z", efield_z, NULL);
- STYPE ("E-zt", efield_zt, NULL);
+ STYPE ("E-x", is->efield_x, NULL);
+ STYPE ("E-xt", is->efield_xt, NULL);
+ STYPE ("E-y", is->efield_y, NULL);
+ STYPE ("E-yt", is->efield_yt, NULL);
+ STYPE ("E-z", is->efield_z, NULL);
+ STYPE ("E-zt", is->efield_zt, NULL);
/* AdResS defined thingies */
CCTYPE ("AdResS parameters");
/* User defined thingies */
CCTYPE ("User defined thingies");
- STYPE ("user1-grps", user1, NULL);
- STYPE ("user2-grps", user2, NULL);
+ STYPE ("user1-grps", is->user1, NULL);
+ STYPE ("user2-grps", is->user2, NULL);
ITYPE ("userint1", ir->userint1, 0);
ITYPE ("userint2", ir->userint2, 0);
ITYPE ("userint3", ir->userint3, 0);
}
opts->couple_moltype = NULL;
- if (strlen(couple_moltype) > 0)
+ if (strlen(is->couple_moltype) > 0)
{
if (ir->efep != efepNO)
{
- opts->couple_moltype = strdup(couple_moltype);
+ opts->couple_moltype = strdup(is->couple_moltype);
if (opts->couple_lam0 == opts->couple_lam1)
{
warning(wi, "The lambda=0 and lambda=1 states for coupling are identical");
{
ir->bExpanded = TRUE;
}
- do_fep_params(ir, fep_lambda, lambda_weights);
+ do_fep_params(ir, is->fep_lambda, is->lambda_weights);
if (ir->bSimTemp) /* done after fep params */
{
do_simtemp_params(ir);
/* WALL PARAMETERS */
- do_wall_params(ir, wall_atomtype, wall_density, opts);
+ do_wall_params(ir, is->wall_atomtype, is->wall_density, opts);
/* ORIENTATION RESTRAINT PARAMETERS */
- if (opts->bOrire && str_nelem(orirefitgrp, MAXPTR, NULL) != 1)
+ if (opts->bOrire && str_nelem(is->orirefitgrp, MAXPTR, NULL) != 1)
{
warning_error(wi, "ERROR: Need one orientation restraint fit group\n");
}
{
dumdub[0][i] = 0;
}
- m = sscanf(deform, "%lf %lf %lf %lf %lf %lf",
+ m = sscanf(is->deform, "%lf %lf %lf %lf %lf %lf",
&(dumdub[0][0]), &(dumdub[0][1]), &(dumdub[0][2]),
&(dumdub[0][3]), &(dumdub[0][4]), &(dumdub[0][5]));
for (i = 0; i < 3; i++)
set_warning_line(wi, mdparin, -1);
- ntau_t = str_nelem(tau_t, MAXPTR, ptr1);
- nref_t = str_nelem(ref_t, MAXPTR, ptr2);
- ntcg = str_nelem(tcgrps, MAXPTR, ptr3);
+ ntau_t = str_nelem(is->tau_t, MAXPTR, ptr1);
+ nref_t = str_nelem(is->ref_t, MAXPTR, ptr2);
+ ntcg = str_nelem(is->tcgrps, MAXPTR, ptr3);
if ((ntau_t != ntcg) || (nref_t != ntcg))
{
gmx_fatal(FARGS, "Invalid T coupling input: %d groups, %d ref-t values and "
}
/* Simulated annealing for each group. There are nr groups */
- nSA = str_nelem(anneal, MAXPTR, ptr1);
+ nSA = str_nelem(is->anneal, MAXPTR, ptr1);
if (nSA == 1 && (ptr1[0][0] == 'n' || ptr1[0][0] == 'N'))
{
nSA = 0;
if (bAnneal)
{
/* Read the other fields too */
- nSA_points = str_nelem(anneal_npoints, MAXPTR, ptr1);
+ nSA_points = str_nelem(is->anneal_npoints, MAXPTR, ptr1);
if (nSA_points != nSA)
{
gmx_fatal(FARGS, "Found %d annealing-npoints values for %d groups\n", nSA_points, nSA);
k += ir->opts.anneal_npoints[i];
}
- nSA_time = str_nelem(anneal_time, MAXPTR, ptr1);
+ nSA_time = str_nelem(is->anneal_time, MAXPTR, ptr1);
if (nSA_time != k)
{
gmx_fatal(FARGS, "Found %d annealing-time values, wanter %d\n", nSA_time, k);
}
- nSA_temp = str_nelem(anneal_temp, MAXPTR, ptr2);
+ nSA_temp = str_nelem(is->anneal_temp, MAXPTR, ptr2);
if (nSA_temp != k)
{
gmx_fatal(FARGS, "Found %d annealing-temp values, wanted %d\n", nSA_temp, k);
if (ir->ePull != epullNO)
{
- make_pull_groups(ir->pull, pull_grp, grps, gnames);
+ make_pull_groups(ir->pull, is->pull_grp, grps, gnames);
make_pull_coords(ir->pull);
}
if (ir->bRot)
{
- make_rotation_groups(ir->rot, rot_grp, grps, gnames);
+ make_rotation_groups(ir->rot, is->rot_grp, grps, gnames);
}
- nacc = str_nelem(acc, MAXPTR, ptr1);
- nacg = str_nelem(accgrps, MAXPTR, ptr2);
+ nacc = str_nelem(is->acc, MAXPTR, ptr1);
+ nacg = str_nelem(is->accgrps, MAXPTR, ptr2);
if (nacg*DIM != nacc)
{
gmx_fatal(FARGS, "Invalid Acceleration input: %d groups and %d acc. values",
}
}
- nfrdim = str_nelem(frdim, MAXPTR, ptr1);
- nfreeze = str_nelem(freeze, MAXPTR, ptr2);
+ nfrdim = str_nelem(is->frdim, MAXPTR, ptr1);
+ nfreeze = str_nelem(is->freeze, MAXPTR, ptr2);
if (nfrdim != DIM*nfreeze)
{
gmx_fatal(FARGS, "Invalid Freezing input: %d groups and %d freeze values",
}
}
- nenergy = str_nelem(energy, MAXPTR, ptr1);
+ nenergy = str_nelem(is->energy, MAXPTR, ptr1);
do_numbering(natoms, groups, nenergy, ptr1, grps, gnames, egcENER,
restnm, egrptpALL_GENREST, bVerbose, wi);
add_wall_energrps(groups, ir->nwall, symtab);
ir->opts.ngener = groups->grps[egcENER].nr;
- nvcm = str_nelem(vcm, MAXPTR, ptr1);
+ nvcm = str_nelem(is->vcm, MAXPTR, ptr1);
bRest =
do_numbering(natoms, groups, nvcm, ptr1, grps, gnames, egcVCM,
restnm, nvcm == 0 ? egrptpALL_GENREST : egrptpPART, bVerbose, wi);
}
}
- nuser = str_nelem(user1, MAXPTR, ptr1);
+ nuser = str_nelem(is->user1, MAXPTR, ptr1);
do_numbering(natoms, groups, nuser, ptr1, grps, gnames, egcUser1,
restnm, egrptpALL_GENREST, bVerbose, wi);
- nuser = str_nelem(user2, MAXPTR, ptr1);
+ nuser = str_nelem(is->user2, MAXPTR, ptr1);
do_numbering(natoms, groups, nuser, ptr1, grps, gnames, egcUser2,
restnm, egrptpALL_GENREST, bVerbose, wi);
- nuser = str_nelem(xtc_grps, MAXPTR, ptr1);
+ nuser = str_nelem(is->xtc_grps, MAXPTR, ptr1);
do_numbering(natoms, groups, nuser, ptr1, grps, gnames, egcXTC,
restnm, egrptpONE, bVerbose, wi);
- nofg = str_nelem(orirefitgrp, MAXPTR, ptr1);
+ nofg = str_nelem(is->orirefitgrp, MAXPTR, ptr1);
do_numbering(natoms, groups, nofg, ptr1, grps, gnames, egcORFIT,
restnm, egrptpALL_GENREST, bVerbose, wi);
/* QMMM input processing */
- nQMg = str_nelem(QMMM, MAXPTR, ptr1);
- nQMmethod = str_nelem(QMmethod, MAXPTR, ptr2);
- nQMbasis = str_nelem(QMbasis, MAXPTR, ptr3);
+ nQMg = str_nelem(is->QMMM, MAXPTR, ptr1);
+ nQMmethod = str_nelem(is->QMmethod, MAXPTR, ptr2);
+ nQMbasis = str_nelem(is->QMbasis, MAXPTR, ptr3);
if ((nQMmethod != nQMg) || (nQMbasis != nQMg))
{
gmx_fatal(FARGS, "Invalid QMMM input: %d groups %d basissets"
eQMbasis_names);
}
- nQMmult = str_nelem(QMmult, MAXPTR, ptr1);
- nQMcharge = str_nelem(QMcharge, MAXPTR, ptr2);
- nbSH = str_nelem(bSH, MAXPTR, ptr3);
+ nQMmult = str_nelem(is->QMmult, MAXPTR, ptr1);
+ nQMcharge = str_nelem(is->QMcharge, MAXPTR, ptr2);
+ nbSH = str_nelem(is->bSH, MAXPTR, ptr3);
snew(ir->opts.QMmult, nr);
snew(ir->opts.QMcharge, nr);
snew(ir->opts.bSH, nr);
ir->opts.bSH[i] = (gmx_strncasecmp(ptr3[i], "Y", 1) == 0);
}
- nCASelec = str_nelem(CASelectrons, MAXPTR, ptr1);
- nCASorb = str_nelem(CASorbitals, MAXPTR, ptr2);
+ nCASelec = str_nelem(is->CASelectrons, MAXPTR, ptr1);
+ nCASorb = str_nelem(is->CASorbitals, MAXPTR, ptr2);
snew(ir->opts.CASelectrons, nr);
snew(ir->opts.CASorbitals, nr);
for (i = 0; i < nr; i++)
}
/* special optimization options */
- nbOPT = str_nelem(bOPT, MAXPTR, ptr1);
- nbTS = str_nelem(bTS, MAXPTR, ptr2);
+ nbOPT = str_nelem(is->bOPT, MAXPTR, ptr1);
+ nbTS = str_nelem(is->bTS, MAXPTR, ptr2);
snew(ir->opts.bOPT, nr);
snew(ir->opts.bTS, nr);
for (i = 0; i < nr; i++)
ir->opts.bOPT[i] = (gmx_strncasecmp(ptr1[i], "Y", 1) == 0);
ir->opts.bTS[i] = (gmx_strncasecmp(ptr2[i], "Y", 1) == 0);
}
- nSAon = str_nelem(SAon, MAXPTR, ptr1);
- nSAoff = str_nelem(SAoff, MAXPTR, ptr2);
- nSAsteps = str_nelem(SAsteps, MAXPTR, ptr3);
+ nSAon = str_nelem(is->SAon, MAXPTR, ptr1);
+ nSAoff = str_nelem(is->SAoff, MAXPTR, ptr2);
+ nSAsteps = str_nelem(is->SAsteps, MAXPTR, ptr3);
snew(ir->opts.SAon, nr);
snew(ir->opts.SAoff, nr);
snew(ir->opts.SAsteps, nr);
nr = groups->grps[egcENER].nr;
snew(ir->opts.egp_flags, nr*nr);
- bExcl = do_egp_flag(ir, groups, "energygrp-excl", egpexcl, EGP_EXCL);
+ bExcl = do_egp_flag(ir, groups, "energygrp-excl", is->egpexcl, EGP_EXCL);
if (bExcl && ir->cutoff_scheme == ecutsVERLET)
{
warning_error(wi, "Energy group exclusions are not (yet) implemented for the Verlet scheme");
warning(wi, "Can not exclude the lattice Coulomb energy between energy groups");
}
- bTable = do_egp_flag(ir, groups, "energygrp-table", egptable, EGP_TABLE);
+ bTable = do_egp_flag(ir, groups, "energygrp-table", is->egptable, EGP_TABLE);
if (bTable && !(ir->vdwtype == evdwUSER) &&
!(ir->coulombtype == eelUSER) && !(ir->coulombtype == eelPMEUSER) &&
!(ir->coulombtype == eelPMEUSERSWITCH))
gmx_fatal(FARGS, "Can only have energy group pair tables in combination with user tables for VdW and/or Coulomb");
}
- decode_cos(efield_x, &(ir->ex[XX]));
- decode_cos(efield_xt, &(ir->et[XX]));
- decode_cos(efield_y, &(ir->ex[YY]));
- decode_cos(efield_yt, &(ir->et[YY]));
- decode_cos(efield_z, &(ir->ex[ZZ]));
- decode_cos(efield_zt, &(ir->et[ZZ]));
+ decode_cos(is->efield_x, &(ir->ex[XX]));
+ decode_cos(is->efield_xt, &(ir->et[XX]));
+ decode_cos(is->efield_y, &(ir->ex[YY]));
+ decode_cos(is->efield_yt, &(ir->et[YY]));
+ decode_cos(is->efield_z, &(ir->ex[ZZ]));
+ decode_cos(is->efield_zt, &(ir->et[ZZ]));
if (ir->bAdress)
{
biod.pnpi.spb.ru / alexxy / gromacs.git / commitdiff