#include "gromacs/mdtypes/inputrec.h"
#include "gromacs/mdtypes/md_enums.h"
#include "gromacs/mdtypes/pull-params.h"
+#include "gromacs/options/options.h"
+#include "gromacs/options/treesupport.h"
#include "gromacs/pbcutil/pbc.h"
#include "gromacs/topology/block.h"
#include "gromacs/topology/ifunc.h"
#include "gromacs/topology/symtab.h"
#include "gromacs/topology/topology.h"
#include "gromacs/utility/cstringutil.h"
+#include "gromacs/utility/exceptions.h"
#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/gmxassert.h"
+#include "gromacs/utility/ikeyvaluetreeerror.h"
+#include "gromacs/utility/keyvaluetree.h"
+#include "gromacs/utility/keyvaluetreetransform.h"
#include "gromacs/utility/smalloc.h"
+#include "gromacs/utility/stringcompare.h"
+#include "gromacs/utility/stringutil.h"
#define MAXPTR 254
#define NOGID 255
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;
couple_lambda_value == ecouplamVDWQ);
}
+namespace
+{
+
+class MdpErrorHandler : public gmx::IKeyValueTreeErrorHandler
+{
+ public:
+ explicit MdpErrorHandler(warninp_t wi)
+ : wi_(wi), mapping_(nullptr)
+ {
+ }
+
+ void setBackMapping(const gmx::IKeyValueTreeBackMapping &mapping)
+ {
+ mapping_ = &mapping;
+ }
+
+ virtual bool onError(gmx::UserInputError *ex, const gmx::KeyValueTreePath &context)
+ {
+ ex->prependContext(gmx::formatString("Error in mdp option \"%s\":",
+ getOptionName(context).c_str()));
+ std::string message = gmx::formatExceptionMessageToString(*ex);
+ warning_error(wi_, message.c_str());
+ return true;
+ }
+
+ private:
+ std::string getOptionName(const gmx::KeyValueTreePath &context)
+ {
+ if (mapping_ != nullptr)
+ {
+ gmx::KeyValueTreePath path = mapping_->originalPath(context);
+ GMX_ASSERT(path.size() == 1, "Inconsistent mapping back to mdp options");
+ return path[0];
+ }
+ GMX_ASSERT(context.size() == 1, "Inconsistent context for mdp option parsing");
+ return context[0];
+ }
+
+ warninp_t wi_;
+ const gmx::IKeyValueTreeBackMapping *mapping_;
+};
+
+} // namespace
+
void get_ir(const char *mdparin, const char *mdparout,
t_inputrec *ir, t_gromppopts *opts,
warninp_t wi)
}
/* Electric fields */
- 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", is->efield_x, NULL);
- CTYPE ("Time dependent (pulsed) electric field. Format is omega, time for pulse");
- CTYPE ("peak, and sigma (width) for pulse. Sigma = 0 removes pulse, leaving");
- CTYPE ("the field to be a cosine function.");
- 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);
+ {
+ gmx::KeyValueTreeObject convertedValues = flatKeyValueTreeFromInpFile(ninp, inp);
+ gmx::KeyValueTreeTransformer transform;
+ transform.rules()->addRule()
+ .keyMatchType("/", gmx::StringCompareType::CaseAndDashInsensitive);
+ ir->efield->initMdpTransform(transform.rules());
+ for (const auto &path : transform.mappedPaths())
+ {
+ GMX_ASSERT(path.size() == 1, "Inconsistent mapping back to mdp options");
+ mark_einp_set(ninp, inp, path[0].c_str());
+ }
+ gmx::Options options;
+ ir->efield->initMdpOptions(&options);
+ MdpErrorHandler errorHandler(wi);
+ auto result
+ = transform.transform(convertedValues, &errorHandler);
+ errorHandler.setBackMapping(result.backMapping());
+ gmx::assignOptionsFromKeyValueTree(&options, result.object(),
+ &errorHandler);
+ }
/* Ion/water position swapping ("computational electrophysiology") */
CCTYPE("Ion/water position swapping for computational electrophysiology setups");
double *nrdf_tc, *nrdf_vcm, nrdf_uc, *nrdf_vcm_sub;
ivec *dof_vcm;
gmx_mtop_atomloop_all_t aloop;
- t_atom *atom;
int mb, mol, ftype, as;
gmx_molblock_t *molb;
gmx_moltype_t *molt;
snew(nrdf2, natoms);
aloop = gmx_mtop_atomloop_all_init(mtop);
+ const t_atom *atom;
while (gmx_mtop_atomloop_all_next(aloop, &i, &atom))
{
nrdf2[i] = 0;
sfree(nrdf_vcm_sub);
}
-static void decode_cos(char *s, t_cosines *cosine)
-{
- char *t;
- char format[STRLEN], f1[STRLEN];
- double a, phi;
- int i;
-
- t = gmx_strdup(s);
- trim(t);
-
- cosine->n = 0;
- cosine->a = NULL;
- cosine->phi = NULL;
- if (strlen(t))
- {
- if (sscanf(t, "%d", &(cosine->n)) != 1)
- {
- gmx_fatal(FARGS, "Cannot parse cosine multiplicity from string '%s'", t);
- }
- if (cosine->n <= 0)
- {
- cosine->n = 0;
- }
- else
- {
- snew(cosine->a, cosine->n);
- snew(cosine->phi, cosine->n);
-
- sprintf(format, "%%*d");
- for (i = 0; (i < cosine->n); i++)
- {
- double gmx_unused canary;
-
- strcpy(f1, format);
- strcat(f1, "%lf%lf%lf");
- if (sscanf(t, f1, &a, &phi, &canary) != 2)
- {
- gmx_fatal(FARGS, "Invalid input for electric field shift: '%s'", t);
- }
- cosine->a[i] = a;
- cosine->phi[i] = phi;
- strcat(format, "%*lf%*lf");
- }
- }
- }
- sfree(t);
-}
-
static gmx_bool do_egp_flag(t_inputrec *ir, gmx_groups_t *groups,
const char *option, const char *val, int flag)
{
gmx_fatal(FARGS, "Can only have energy group pair tables in combination with user tables for VdW and/or Coulomb");
}
- 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]));
-
for (i = 0; (i < grps->nr); i++)
{
sfree(gnames[i]);
rvec acc;
gmx_mtop_atomloop_block_t aloopb;
gmx_mtop_atomloop_all_t aloop;
- t_atom *atom;
ivec AbsRef;
char warn_buf[STRLEN];
bCharge = FALSE;
aloopb = gmx_mtop_atomloop_block_init(sys);
+ const t_atom *atom;
while (gmx_mtop_atomloop_block_next(aloopb, &atom, &nmol))
{
if (atom->q != 0 || atom->qB != 0)
clear_rvec(acc);
snew(mgrp, sys->groups.grps[egcACC].nr);
aloop = gmx_mtop_atomloop_all_init(sys);
+ const t_atom *atom;
while (gmx_mtop_atomloop_all_next(aloop, &i, &atom))
{
mgrp[ggrpnr(&sys->groups, egcACC, i)] += atom->m;
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff