#include "gromacs/utility/cstringutil.h"
#include "gromacs/utility/fatalerror.h"
#include "gromacs/utility/gmxassert.h"
+#include "gromacs/utility/logger.h"
#include "gromacs/utility/smalloc.h"
#include "gromacs/utility/strconvert.h"
static bool calc_vsite4fd_param(InteractionOfType* vsite,
gmx::ArrayRef<const VsiteBondedInteraction> bonds,
- gmx::ArrayRef<const VsiteBondedInteraction> angles)
+ gmx::ArrayRef<const VsiteBondedInteraction> angles,
+ const gmx::MDLogger& logger)
{
/* i = virtual site | ,k
* j = 1st bonded heavy atom | i-j-m
cosakm = (std::cos(akjm) - std::cos(aijk) * std::cos(aijm)) / (std::sin(aijk) * std::sin(aijm));
if (cosakl < -1 || cosakl > 1 || cosakm < -1 || cosakm > 1)
{
- fprintf(stderr, "virtual site %d: angle ijk = %f, angle ijl = %f, angle ijm = %f\n",
- vsite->ai() + 1, RAD2DEG * aijk, RAD2DEG * aijl, RAD2DEG * aijm);
+ GMX_LOG(logger.warning)
+ .asParagraph()
+ .appendTextFormatted(
+ "virtual site %d: angle ijk = %f, angle ijl = %f, angle ijm = %f",
+ vsite->ai() + 1, RAD2DEG * aijk, RAD2DEG * aijl, RAD2DEG * aijm);
gmx_fatal(FARGS,
"invalid construction in calc_vsite4fd for atom %d: "
"cosakl=%f, cosakm=%f\n",
static bool calc_vsite4fdn_param(InteractionOfType* vsite,
gmx::ArrayRef<const VsiteBondedInteraction> bonds,
- gmx::ArrayRef<const VsiteBondedInteraction> angles)
+ gmx::ArrayRef<const VsiteBondedInteraction> angles,
+ const gmx::MDLogger& logger)
{
/* i = virtual site | ,k
* j = 1st bonded heavy atom | i-j-m
if (fabs(pl) < 1000 * GMX_REAL_MIN || fabs(pm) < 1000 * GMX_REAL_MIN)
{
- fprintf(stderr, "virtual site %d: angle ijk = %f, angle ijl = %f, angle ijm = %f\n",
- vsite->ai() + 1, RAD2DEG * aijk, RAD2DEG * aijl, RAD2DEG * aijm);
+ GMX_LOG(logger.warning)
+ .asParagraph()
+ .appendTextFormatted(
+ "virtual site %d: angle ijk = %f, angle ijl = %f, angle ijm = %f",
+ vsite->ai() + 1, RAD2DEG * aijk, RAD2DEG * aijl, RAD2DEG * aijm);
gmx_fatal(FARGS,
"invalid construction in calc_vsite4fdn for atom %d: "
"pl=%f, pm=%f\n",
}
-int set_vsites(bool bVerbose, t_atoms* atoms, PreprocessingAtomTypes* atypes, gmx::ArrayRef<InteractionsOfType> plist)
+int set_vsites(bool bVerbose,
+ t_atoms* atoms,
+ PreprocessingAtomTypes* atypes,
+ gmx::ArrayRef<InteractionsOfType> plist,
+ const gmx::MDLogger& logger)
{
int ftype;
int nvsite, nrset;
{
if (bVerbose && bFirst)
{
- fprintf(stderr, "Calculating parameters for virtual sites\n");
+ GMX_LOG(logger.info)
+ .asParagraph()
+ .appendTextFormatted("Calculating parameters for virtual sites");
bFirst = FALSE;
}
break;
case F_VSITE4FD:
bERROR = calc_vsite4fd_param(¶m, allVsiteBondeds.bonds,
- allVsiteBondeds.angles);
+ allVsiteBondeds.angles, logger);
break;
case F_VSITE4FDN:
bERROR = calc_vsite4fdn_param(¶m, allVsiteBondeds.bonds,
- allVsiteBondeds.angles);
+ allVsiteBondeds.angles, logger);
break;
default:
gmx_fatal(FARGS,
return nvsite;
}
-void set_vsites_ptype(bool bVerbose, gmx_moltype_t* molt)
+void set_vsites_ptype(bool bVerbose, gmx_moltype_t* molt, const gmx::MDLogger& logger)
{
int ftype, i;
if (bVerbose)
{
- fprintf(stderr, "Setting particle type to V for virtual sites\n");
+ GMX_LOG(logger.info)
+ .asParagraph()
+ .appendTextFormatted("Setting particle type to V for virtual sites");
}
for (ftype = 0; ftype < F_NRE; ftype++)
{
if (debug && nrd)
{
- fprintf(stderr, "doing %d %s virtual sites\n", (nrd / (nra + 1)),
- interaction_function[ftype].longname);
+ GMX_LOG(logger.info)
+ .asParagraph()
+ .appendTextFormatted("doing %d %s virtual sites", (nrd / (nra + 1)),
+ interaction_function[ftype].longname);
}
for (i = 0; (i < nrd);)
int interactionIndex_;
};
-static void check_vsite_constraints(gmx::ArrayRef<InteractionsOfType> plist, int cftype, const int vsite_type[])
+static void check_vsite_constraints(gmx::ArrayRef<InteractionsOfType> plist,
+ int cftype,
+ const int vsite_type[],
+ const gmx::MDLogger& logger)
{
int n = 0;
for (const auto& param : plist[cftype].interactionTypes)
int atom = atoms[k];
if (vsite_type[atom] != NOTSET)
{
- fprintf(stderr, "ERROR: Cannot have constraint (%d-%d) with virtual site (%d)\n",
- param.ai() + 1, param.aj() + 1, atom + 1);
+ GMX_LOG(logger.info)
+ .asParagraph()
+ .appendTextFormatted(
+ "ERROR: Cannot have constraint (%d-%d) with virtual site (%d)",
+ param.ai() + 1, param.aj() + 1, atom + 1);
n++;
}
}
static void clean_vsite_bonds(gmx::ArrayRef<InteractionsOfType> plist,
gmx::ArrayRef<const VsiteAtomMapping> pindex,
int cftype,
- const int vsite_type[])
+ const int vsite_type[],
+ const gmx::MDLogger& logger)
{
int ftype, nOut;
int nconverted, nremoved;
if (nremoved)
{
- fprintf(stderr, "Removed %4d %15ss with virtual sites, %zu left\n", nremoved,
- interaction_function[cftype].longname, ps->size());
+ GMX_LOG(logger.info)
+ .asParagraph()
+ .appendTextFormatted("Removed %4d %15ss with virtual sites, %zu left", nremoved,
+ interaction_function[cftype].longname, ps->size());
}
if (nconverted)
{
- fprintf(stderr, "Converted %4d %15ss with virtual sites to connections, %zu left\n",
- nconverted, interaction_function[cftype].longname, ps->size());
+ GMX_LOG(logger.info)
+ .asParagraph()
+ .appendTextFormatted(
+ "Converted %4d %15ss with virtual sites to connections, %zu left",
+ nconverted, interaction_function[cftype].longname, ps->size());
}
if (nOut)
{
- fprintf(stderr,
- "Warning: removed %d %ss with vsite with %s construction\n"
- " This vsite construction does not guarantee constant "
- "bond-length\n"
- " If the constructions were generated by pdb2gmx ignore "
- "this warning\n",
- nOut, interaction_function[cftype].longname, interaction_function[F_VSITE3OUT].longname);
+ GMX_LOG(logger.info)
+ .asParagraph()
+ .appendTextFormatted(
+ "Warning: removed %d %ss with vsite with %s construction\n"
+ " This vsite construction does not guarantee constant "
+ "bond-length\n"
+ " If the constructions were generated by pdb2gmx ignore "
+ "this warning",
+ nOut, interaction_function[cftype].longname,
+ interaction_function[F_VSITE3OUT].longname);
}
}
gmx::ArrayRef<VsiteAtomMapping> pindex,
int cftype,
const int vsite_type[],
- gmx::ArrayRef<const Atom2VsiteConnection> at2vc)
+ gmx::ArrayRef<const Atom2VsiteConnection> at2vc,
+ const gmx::MDLogger& logger)
{
int atom, at1, at2;
InteractionsOfType* ps;
if (oldSize != gmx::ssize(*ps))
{
- fprintf(stderr, "Removed %4zu %15ss with virtual sites, %zu left\n", oldSize - ps->size(),
- interaction_function[cftype].longname, ps->size());
+ GMX_LOG(logger.info)
+ .asParagraph()
+ .appendTextFormatted("Removed %4zu %15ss with virtual sites, %zu left",
+ oldSize - ps->size(), interaction_function[cftype].longname,
+ ps->size());
}
}
static void clean_vsite_dihs(gmx::ArrayRef<InteractionsOfType> plist,
gmx::ArrayRef<const VsiteAtomMapping> pindex,
int cftype,
- const int vsite_type[])
+ const int vsite_type[],
+ const gmx::MDLogger& logger)
{
InteractionsOfType* ps;
if (oldSize != gmx::ssize(*ps))
{
- fprintf(stderr, "Removed %4zu %15ss with virtual sites, %zu left\n", oldSize - ps->size(),
- interaction_function[cftype].longname, ps->size());
+ GMX_LOG(logger.info)
+ .asParagraph()
+ .appendTextFormatted("Removed %4zu %15ss with virtual sites, %zu left",
+ oldSize - ps->size(), interaction_function[cftype].longname,
+ ps->size());
}
}
// TODO use gmx::compat::optional for pindex.
-void clean_vsite_bondeds(gmx::ArrayRef<InteractionsOfType> plist, int natoms, bool bRmVSiteBds)
+void clean_vsite_bondeds(gmx::ArrayRef<InteractionsOfType> plist,
+ int natoms,
+ bool bRmVSiteBds,
+ const gmx::MDLogger& logger)
{
int nvsite, vsite;
int* vsite_type;
/* the rest only if we have virtual sites: */
if (nvsite)
{
- fprintf(stderr, "Cleaning up constraints %swith virtual sites\n",
- bRmVSiteBds ? "and constant bonded interactions " : "");
+ GMX_LOG(logger.info)
+ .asParagraph()
+ .appendTextFormatted("Cleaning up constraints %swith virtual sites",
+ bRmVSiteBds ? "and constant bonded interactions " : "");
/* Make a reverse list to avoid ninteractions^2 operations */
at2vc = make_at2vsitecon(natoms, plist);
{
if (interaction_function[ftype].flags & (IF_BTYPE | IF_CONSTRAINT))
{
- clean_vsite_bonds(plist, pindex, ftype, vsite_type);
+ clean_vsite_bonds(plist, pindex, ftype, vsite_type, logger);
}
else if (interaction_function[ftype].flags & IF_ATYPE)
{
- clean_vsite_angles(plist, pindex, ftype, vsite_type, at2vc);
+ clean_vsite_angles(plist, pindex, ftype, vsite_type, at2vc, logger);
}
else if ((ftype == F_PDIHS) || (ftype == F_IDIHS))
{
- clean_vsite_dihs(plist, pindex, ftype, vsite_type);
+ clean_vsite_dihs(plist, pindex, ftype, vsite_type, logger);
}
}
}
{
if (interaction_function[ftype].flags & IF_CONSTRAINT)
{
- check_vsite_constraints(plist, ftype, vsite_type);
+ check_vsite_constraints(plist, ftype, vsite_type, logger);
}
}
}
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff