#include "gromacs/utility/cstringutil.h"
#include "gromacs/utility/exceptions.h"
#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/filestream.h"
#include "gromacs/utility/futil.h"
#include "gromacs/utility/gmxassert.h"
#include "gromacs/utility/keyvaluetreebuilder.h"
#include "gromacs/utility/listoflists.h"
+#include "gromacs/utility/logger.h"
+#include "gromacs/utility/loggerbuilder.h"
#include "gromacs/utility/mdmodulenotification.h"
#include "gromacs/utility/smalloc.h"
#include "gromacs/utility/snprintf.h"
return n;
}
-static int check_atom_names(const char* fn1, const char* fn2, gmx_mtop_t* mtop, const t_atoms* at)
+static int check_atom_names(const char* fn1,
+ const char* fn2,
+ gmx_mtop_t* mtop,
+ const t_atoms* at,
+ const gmx::MDLogger& logger)
{
int m, i, j, nmismatch;
t_atoms* tat;
-#define MAXMISMATCH 20
+
+ constexpr int c_maxNumberOfMismatches = 20;
if (mtop->natoms != at->nr)
{
{
if (strcmp(*(tat->atomname[j]), *(at->atomname[i])) != 0)
{
- if (nmismatch < MAXMISMATCH)
+ if (nmismatch < c_maxNumberOfMismatches)
{
- fprintf(stderr,
- "Warning: atom name %d in %s and %s does not match (%s - %s)\n",
- i + 1, fn1, fn2, *(tat->atomname[j]), *(at->atomname[i]));
+ GMX_LOG(logger.warning)
+ .asParagraph()
+ .appendTextFormatted(
+ "atom name %d in %s and %s does not match (%s - %s)", i + 1,
+ fn1, fn2, *(tat->atomname[j]), *(at->atomname[i]));
}
- else if (nmismatch == MAXMISMATCH)
+ else if (nmismatch == c_maxNumberOfMismatches)
{
- fprintf(stderr, "(more than %d non-matching atom names)\n", MAXMISMATCH);
+ GMX_LOG(logger.warning)
+ .asParagraph()
+ .appendTextFormatted("(more than %d non-matching atom names)",
+ c_maxNumberOfMismatches);
}
nmismatch++;
}
int i, a1, a2, w_a1, w_a2, j;
real twopi2, limit2, fc, re, m1, m2, period2, w_period2;
bool bFound, bWater, bWarn;
- char warn_buf[STRLEN];
/* Get the interaction parameters */
gmx::ArrayRef<const t_iparams> ip = mtop->ffparams.iparams;
bWarn = (w_period2 < gmx::square(min_steps_warn * dt));
/* A check that would recognize most water models */
bWater = ((*w_moltype->atoms.atomname[0])[0] == 'O' && w_moltype->atoms.nr <= 5);
- sprintf(warn_buf,
+ std::string warningMessage = gmx::formatString(
"The bond in molecule-type %s between atoms %d %s and %d %s has an estimated "
"oscillational period of %.1e ps, which is less than %d times the time step of "
"%.1e ps.\n"
: "Maybe you forgot to change the constraints mdp option.");
if (bWarn)
{
- warning(wi, warn_buf);
+ warning(wi, warningMessage.c_str());
}
else
{
- warning_note(wi, warn_buf);
+ warning_note(wi, warningMessage.c_str());
}
}
}
static void check_shells_inputrec(gmx_mtop_t* mtop, t_inputrec* ir, warninp* wi)
{
- int nshells = 0;
- char warn_buf[STRLEN];
+ int nshells = 0;
for (const AtomProxy atomP : AtomRange(*mtop))
{
if ((nshells > 0) && (ir->nstcalcenergy != 1))
{
set_warning_line(wi, "unknown", -1);
- snprintf(warn_buf, STRLEN, "There are %d shells, changing nstcalcenergy from %d to 1",
- nshells, ir->nstcalcenergy);
+ std::string warningMessage = gmx::formatString(
+ "There are %d shells, changing nstcalcenergy from %d to 1", nshells, ir->nstcalcenergy);
ir->nstcalcenergy = 1;
- warning(wi, warn_buf);
+ warning(wi, warningMessage.c_str());
}
}
double* reppow,
real* fudgeQQ,
gmx_bool bMorse,
- warninp* wi)
+ warninp* wi,
+ const gmx::MDLogger& logger)
{
std::vector<gmx_molblock_t> molblock;
int i, nmismatch;
bool ffParametrizedWithHBondConstraints;
- char buf[STRLEN];
- char warn_buf[STRLEN];
/* TOPOLOGY processing */
sys->name = do_top(bVerbose, topfile, topppfile, opts, bZero, &(sys->symtab), interactions,
if (i > 0)
{
set_warning_line(wi, "unknown", -1);
- sprintf(warn_buf, "disre = no, removed %d distance restraints", i);
- warning_note(wi, warn_buf);
+ std::string warningMessage =
+ gmx::formatString("disre = no, removed %d distance restraints", i);
+ warning_note(wi, warningMessage.c_str());
}
}
if (!opts->bOrire)
if (i > 0)
{
set_warning_line(wi, "unknown", -1);
- sprintf(warn_buf, "orire = no, removed %d orientation restraints", i);
- warning_note(wi, warn_buf);
+ std::string warningMessage =
+ gmx::formatString("orire = no, removed %d orientation restraints", i);
+ warning_note(wi, warningMessage.c_str());
}
}
/* COORDINATE file processing */
if (bVerbose)
{
- fprintf(stderr, "processing coordinates...\n");
+ GMX_LOG(logger.info).asParagraph().appendTextFormatted("processing coordinates...");
}
t_topology* conftop;
/* This call fixes the box shape for runs with pressure scaling */
set_box_rel(ir, state);
- nmismatch = check_atom_names(topfile, confin, sys, &conftop->atoms);
+ nmismatch = check_atom_names(topfile, confin, sys, &conftop->atoms, logger);
done_top(conftop);
sfree(conftop);
if (nmismatch)
{
- sprintf(buf,
+ std::string warningMessage = gmx::formatString(
"%d non-matching atom name%s\n"
"atom names from %s will be used\n"
"atom names from %s will be ignored\n",
nmismatch, (nmismatch == 1) ? "" : "s", topfile, confin);
- warning(wi, buf);
+ warning(wi, warningMessage.c_str());
}
/* Do more checks, mostly related to constraints */
if (bVerbose)
{
- fprintf(stderr, "double-checking input for internal consistency...\n");
+ GMX_LOG(logger.info)
+ .asParagraph()
+ .appendTextFormatted("double-checking input for internal consistency...");
}
{
bool bHasNormalConstraints =
if (opts->seed == -1)
{
opts->seed = static_cast<int>(gmx::makeRandomSeed());
- fprintf(stderr, "Setting gen_seed to %d\n", opts->seed);
+ GMX_LOG(logger.info).asParagraph().appendTextFormatted("Setting gen_seed to %d", opts->seed);
}
state->flags |= (1 << estV);
maxwell_speed(opts->tempi, opts->seed, sys, state->v.rvec_array());
t_inputrec* ir,
t_state* state,
gmx_mtop_t* sys,
- const gmx_output_env_t* oenv)
+ const gmx_output_env_t* oenv,
+ const gmx::MDLogger& logger)
/* If fr_time == -1 read the last frame available which is complete */
{
bool bReadVel;
bReadVel = (bNeedVel && !bGenVel);
- fprintf(stderr, "Reading Coordinates%s and Box size from old trajectory\n",
- bReadVel ? ", Velocities" : "");
+ GMX_LOG(logger.info)
+ .asParagraph()
+ .appendTextFormatted("Reading Coordinates%s and Box size from old trajectory",
+ bReadVel ? ", Velocities" : "");
if (fr_time == -1)
{
- fprintf(stderr, "Will read whole trajectory\n");
+ GMX_LOG(logger.info).asParagraph().appendTextFormatted("Will read whole trajectory");
}
else
{
- fprintf(stderr, "Will read till time %g\n", fr_time);
+ GMX_LOG(logger.info).asParagraph().appendTextFormatted("Will read till time %g", fr_time);
}
if (!bReadVel)
{
if (bGenVel)
{
- fprintf(stderr,
- "Velocities generated: "
- "ignoring velocities in input trajectory\n");
+ GMX_LOG(logger.info)
+ .asParagraph()
+ .appendTextFormatted(
+ "Velocities generated: "
+ "ignoring velocities in input trajectory");
}
read_first_frame(oenv, &fp, slog, &fr, TRX_NEED_X);
}
if (!fr.bV)
{
- fprintf(stderr,
- "\n"
- "WARNING: Did not find a frame with velocities in file %s,\n"
- " all velocities will be set to zero!\n\n",
- slog);
+ GMX_LOG(logger.warning)
+ .asParagraph()
+ .appendTextFormatted(
+ "WARNING: Did not find a frame with velocities in file %s,\n"
+ " all velocities will be set to zero!",
+ slog);
for (auto& vi : makeArrayRef(state->v))
{
vi = { 0, 0, 0 };
*/
set_box_rel(ir, state);
- fprintf(stderr, "Using frame at t = %g ps\n", use_time);
- fprintf(stderr, "Starting time for run is %g ps\n", ir->init_t);
+ GMX_LOG(logger.info).asParagraph().appendTextFormatted("Using frame at t = %g ps", use_time);
+ GMX_LOG(logger.info).asParagraph().appendTextFormatted("Starting time for run is %g ps", ir->init_t);
if ((ir->epc != epcNO || ir->etc == etcNOSEHOOVER) && ener)
{
int rc_scaling,
PbcType pbcType,
rvec com,
- warninp* wi)
+ warninp* wi,
+ const gmx::MDLogger& logger)
{
gmx_bool* hadAtom;
rvec * x, *v;
t_topology* top;
matrix box, invbox;
int natoms, npbcdim = 0;
- char warn_buf[STRLEN];
int a, nat_molb;
t_atom* atom;
sfree(top);
if (natoms != mtop->natoms)
{
- sprintf(warn_buf,
+ std::string warningMessage = gmx::formatString(
"The number of atoms in %s (%d) does not match the number of atoms in the topology "
"(%d). Will assume that the first %d atoms in the topology and %s match.",
fn, natoms, mtop->natoms, std::min(mtop->natoms, natoms), fn);
- warning(wi, warn_buf);
+ warning(wi, warningMessage.c_str());
}
npbcdim = numPbcDimensions(pbcType);
{
com[j] = sum[j] / totmass;
}
- fprintf(stderr,
- "The center of mass of the position restraint coord's is %6.3f %6.3f %6.3f\n",
- com[XX], com[YY], com[ZZ]);
+ GMX_LOG(logger.info)
+ .asParagraph()
+ .appendTextFormatted(
+ "The center of mass of the position restraint coord's is %6.3f %6.3f %6.3f",
+ com[XX], com[YY], com[ZZ]);
}
if (rc_scaling != erscNO)
PbcType pbcType,
rvec com,
rvec comB,
- warninp* wi)
+ warninp* wi,
+ const gmx::MDLogger& logger)
{
- read_posres(mtop, mi, FALSE, fnA, rc_scaling, pbcType, com, wi);
+ read_posres(mtop, mi, FALSE, fnA, rc_scaling, pbcType, com, wi, logger);
/* It is safer to simply read the b-state posres rather than trying
* to be smart and copy the positions.
*/
- read_posres(mtop, mi, TRUE, fnB, rc_scaling, pbcType, comB, wi);
+ read_posres(mtop, mi, TRUE, fnB, rc_scaling, pbcType, comB, wi, logger);
}
-static void set_wall_atomtype(PreprocessingAtomTypes* at, t_gromppopts* opts, t_inputrec* ir, warninp* wi)
+static void set_wall_atomtype(PreprocessingAtomTypes* at,
+ t_gromppopts* opts,
+ t_inputrec* ir,
+ warninp* wi,
+ const gmx::MDLogger& logger)
{
- int i;
- char warn_buf[STRLEN];
+ int i;
if (ir->nwall > 0)
{
- fprintf(stderr, "Searching the wall atom type(s)\n");
+ GMX_LOG(logger.info).asParagraph().appendTextFormatted("Searching the wall atom type(s)");
}
for (i = 0; i < ir->nwall; i++)
{
ir->wall_atomtype[i] = at->atomTypeFromName(opts->wall_atomtype[i]);
if (ir->wall_atomtype[i] == NOTSET)
{
- sprintf(warn_buf, "Specified wall atom type %s is not defined", opts->wall_atomtype[i]);
- warning_error(wi, warn_buf);
+ std::string warningMessage = gmx::formatString(
+ "Specified wall atom type %s is not defined", opts->wall_atomtype[i]);
+ warning_error(wi, warningMessage.c_str());
}
}
}
static int count_constraints(const gmx_mtop_t* mtop, gmx::ArrayRef<const MoleculeInformation> mi, warninp* wi)
{
- int count, count_mol;
- char buf[STRLEN];
+ int count, count_mol;
count = 0;
for (const gmx_molblock_t& molb : mtop->molblock)
if (count_mol > nrdf_internal(&mi[molb.type].atoms))
{
- sprintf(buf,
+ std::string warningMessage = gmx::formatString(
"Molecule type '%s' has %d constraints.\n"
"For stability and efficiency there should not be more constraints than "
"internal number of degrees of freedom: %d.\n",
*mi[molb.type].name, count_mol, nrdf_internal(&mi[molb.type].atoms));
- warning(wi, buf);
+ warning(wi, warningMessage.c_str());
}
count += molb.nmol * count_mol;
}
if (bNoCoupl)
{
- char buf[STRLEN];
-
- sprintf(buf,
+ std::string warningMessage = gmx::formatString(
"Some temperature coupling groups do not use temperature coupling. We will assume "
"their temperature is not more than %.3f K. If their temperature is higher, the "
"energy error and the Verlet buffer might be underestimated.",
ref_t);
- warning(wi, buf);
+ warning(wi, warningMessage.c_str());
}
return ref_t;
/* Checks if there are unbound atoms in moleculetype molt.
* Prints a note for each unbound atoms and a warning if any is present.
*/
-static void checkForUnboundAtoms(const gmx_moltype_t* molt, gmx_bool bVerbose, warninp* wi)
+static void checkForUnboundAtoms(const gmx_moltype_t* molt, gmx_bool bVerbose, warninp* wi, const gmx::MDLogger& logger)
{
const t_atoms* atoms = &molt->atoms;
{
if (bVerbose)
{
- fprintf(stderr,
- "\nAtom %d '%s' in moleculetype '%s' is not bound by a potential or "
- "constraint to any other atom in the same moleculetype.\n",
- a + 1, *atoms->atomname[a], *molt->name);
+ GMX_LOG(logger.warning)
+ .asParagraph()
+ .appendTextFormatted(
+ "Atom %d '%s' in moleculetype '%s' is not bound by a potential or "
+ "constraint to any other atom in the same moleculetype.",
+ a + 1, *atoms->atomname[a], *molt->name);
}
numDanglingAtoms++;
}
if (numDanglingAtoms > 0)
{
- char buf[STRLEN];
- sprintf(buf,
+ std::string warningMessage = gmx::formatString(
"In moleculetype '%s' %d atoms are not bound by a potential or constraint to any "
"other atom in the same moleculetype. Although technically this might not cause "
"issues in a simulation, this often means that the user forgot to add a "
"bond/potential/constraint or put multiple molecules in the same moleculetype "
"definition by mistake. Run with -v to get information for each atom.",
*molt->name, numDanglingAtoms);
- warning_note(wi, buf);
+ warning_note(wi, warningMessage.c_str());
}
}
/* Checks all moleculetypes for unbound atoms */
-static void checkForUnboundAtoms(const gmx_mtop_t* mtop, gmx_bool bVerbose, warninp* wi)
+static void checkForUnboundAtoms(const gmx_mtop_t* mtop, gmx_bool bVerbose, warninp* wi, const gmx::MDLogger& logger)
{
for (const gmx_moltype_t& molt : mtop->moltype)
{
- checkForUnboundAtoms(&molt, bVerbose, wi);
+ checkForUnboundAtoms(&molt, bVerbose, wi, logger);
}
}
}
}
-static void set_verlet_buffer(const gmx_mtop_t* mtop, t_inputrec* ir, real buffer_temp, matrix box, warninp* wi)
+static void set_verlet_buffer(const gmx_mtop_t* mtop,
+ t_inputrec* ir,
+ real buffer_temp,
+ matrix box,
+ warninp* wi,
+ const gmx::MDLogger& logger)
{
- char warn_buf[STRLEN];
-
- printf("Determining Verlet buffer for a tolerance of %g kJ/mol/ps at %g K\n", ir->verletbuf_tol,
- buffer_temp);
+ GMX_LOG(logger.info)
+ .asParagraph()
+ .appendTextFormatted(
+ "Determining Verlet buffer for a tolerance of %g kJ/mol/ps at %g K",
+ ir->verletbuf_tol, buffer_temp);
/* Calculate the buffer size for simple atom vs atoms list */
VerletbufListSetup listSetup1x1;
const int n_nonlin_vsite = countNonlinearVsites(*mtop);
if (n_nonlin_vsite > 0)
{
- sprintf(warn_buf,
+ std::string warningMessage = gmx::formatString(
"There are %d non-linear virtual site constructions. Their contribution to the "
"energy error is approximated. In most cases this does not affect the error "
"significantly.",
n_nonlin_vsite);
- warning_note(wi, warn_buf);
+ warning_note(wi, warningMessage);
}
- printf("Calculated rlist for %dx%d atom pair-list as %.3f nm, buffer size %.3f nm\n", 1, 1,
- rlist_1x1, rlist_1x1 - std::max(ir->rvdw, ir->rcoulomb));
+ GMX_LOG(logger.info)
+ .asParagraph()
+ .appendTextFormatted(
+ "Calculated rlist for %dx%d atom pair-list as %.3f nm, buffer size %.3f nm", 1,
+ 1, rlist_1x1, rlist_1x1 - std::max(ir->rvdw, ir->rcoulomb));
- printf("Set rlist, assuming %dx%d atom pair-list, to %.3f nm, buffer size %.3f nm\n",
- listSetup4x4.cluster_size_i, listSetup4x4.cluster_size_j, ir->rlist,
- ir->rlist - std::max(ir->rvdw, ir->rcoulomb));
+ GMX_LOG(logger.info)
+ .asParagraph()
+ .appendTextFormatted(
+ "Set rlist, assuming %dx%d atom pair-list, to %.3f nm, buffer size %.3f nm",
+ listSetup4x4.cluster_size_i, listSetup4x4.cluster_size_j, ir->rlist,
+ ir->rlist - std::max(ir->rvdw, ir->rcoulomb));
- printf("Note that mdrun will redetermine rlist based on the actual pair-list setup\n");
+ GMX_LOG(logger.info)
+ .asParagraph()
+ .appendTextFormatted(
+ "Note that mdrun will redetermine rlist based on the actual pair-list setup");
if (gmx::square(ir->rlist) >= max_cutoff2(ir->pbcType, box))
{
gmx_output_env_t* oenv;
gmx_bool bVerbose = FALSE;
warninp* wi;
- char warn_buf[STRLEN];
t_filenm fnm[] = { { efMDP, nullptr, nullptr, ffREAD },
{ efMDP, "-po", "mdout", ffWRITE },
snew(opts->include, STRLEN);
snew(opts->define, STRLEN);
+ gmx::LoggerBuilder builder;
+ builder.addTargetStream(gmx::MDLogger::LogLevel::Info, &gmx::TextOutputFile::standardOutput());
+ builder.addTargetStream(gmx::MDLogger::LogLevel::Warning, &gmx::TextOutputFile::standardError());
+ gmx::LoggerOwner logOwner(builder.build());
+ const gmx::MDLogger logger(logOwner.logger());
+
+
wi = init_warning(TRUE, maxwarn);
/* PARAMETER file processing */
if (bVerbose)
{
- fprintf(stderr, "checking input for internal consistency...\n");
+ GMX_LOG(logger.info)
+ .asParagraph()
+ .appendTextFormatted("checking input for internal consistency...");
}
check_ir(mdparin, mdModules.notifier(), ir, opts, wi);
if (ir->ld_seed == -1)
{
ir->ld_seed = static_cast<int>(gmx::makeRandomSeed());
- fprintf(stderr, "Setting the LD random seed to %" PRId64 "\n", ir->ld_seed);
+ GMX_LOG(logger.info)
+ .asParagraph()
+ .appendTextFormatted("Setting the LD random seed to %" PRId64 "", ir->ld_seed);
}
if (ir->expandedvals->lmc_seed == -1)
{
ir->expandedvals->lmc_seed = static_cast<int>(gmx::makeRandomSeed());
- fprintf(stderr, "Setting the lambda MC random seed to %d\n", ir->expandedvals->lmc_seed);
+ GMX_LOG(logger.info)
+ .asParagraph()
+ .appendTextFormatted("Setting the lambda MC random seed to %d", ir->expandedvals->lmc_seed);
}
bNeedVel = EI_STATE_VELOCITY(ir->eI);
bGenVel = (bNeedVel && opts->bGenVel);
if (bGenVel && ir->bContinuation)
{
- sprintf(warn_buf,
+ std::string warningMessage = gmx::formatString(
"Generating velocities is inconsistent with attempting "
"to continue a previous run. Choose only one of "
"gen-vel = yes and continuation = yes.");
- warning_error(wi, warn_buf);
+ warning_error(wi, warningMessage);
}
std::array<InteractionsOfType, F_NRE> interactions;
t_state state;
new_status(fn, opt2fn_null("-pp", NFILE, fnm), opt2fn("-c", NFILE, fnm), opts, ir, bZero,
bGenVel, bVerbose, &state, &atypes, &sys, &mi, &intermolecular_interactions,
- interactions, &comb, &reppow, &fudgeQQ, opts->bMorse, wi);
+ interactions, &comb, &reppow, &fudgeQQ, opts->bMorse, wi, logger);
if (debug)
{
{
if (ir->eI == eiCG || ir->eI == eiLBFGS)
{
- sprintf(warn_buf, "Can not do %s with %s, use %s", EI(ir->eI),
- econstr_names[econtSHAKE], econstr_names[econtLINCS]);
- warning_error(wi, warn_buf);
+ std::string warningMessage =
+ gmx::formatString("Can not do %s with %s, use %s", EI(ir->eI),
+ econstr_names[econtSHAKE], econstr_names[econtLINCS]);
+ warning_error(wi, warningMessage);
}
if (ir->bPeriodicMols)
{
- sprintf(warn_buf, "Can not do periodic molecules with %s, use %s",
- econstr_names[econtSHAKE], econstr_names[econtLINCS]);
- warning_error(wi, warn_buf);
+ std::string warningMessage =
+ gmx::formatString("Can not do periodic molecules with %s, use %s",
+ econstr_names[econtSHAKE], econstr_names[econtLINCS]);
+ warning_error(wi, warningMessage);
}
}
{
if (ir->epc == epcPARRINELLORAHMAN || ir->epc == epcMTTK)
{
- sprintf(warn_buf,
+ std::string warningMessage = gmx::formatString(
"You are combining position restraints with %s pressure coupling, which can "
"lead to instabilities. If you really want to combine position restraints with "
"pressure coupling, we suggest to use %s pressure coupling instead.",
EPCOUPLTYPE(ir->epc), EPCOUPLTYPE(epcBERENDSEN));
- warning_note(wi, warn_buf);
+ warning_note(wi, warningMessage);
}
const char* fn = opt2fn("-r", NFILE, fnm);
if (bVerbose)
{
- fprintf(stderr, "Reading position restraint coords from %s", fn);
- if (strcmp(fn, fnB) == 0)
- {
- fprintf(stderr, "\n");
- }
- else
+ std::string message = gmx::formatString("Reading position restraint coords from %s", fn);
+ if (strcmp(fn, fnB) != 0)
{
- fprintf(stderr, " and %s\n", fnB);
+ message += gmx::formatString(" and %s", fnB);
}
+ GMX_LOG(logger.info).asParagraph().appendText(message);
}
gen_posres(&sys, mi, fn, fnB, ir->refcoord_scaling, ir->pbcType, ir->posres_com,
- ir->posres_comB, wi);
+ ir->posres_comB, wi, logger);
}
/* If we are using CMAP, setup the pre-interpolation grid */
interactions[F_CMAP].cmap, &sys.ffparams.cmap_grid);
}
- set_wall_atomtype(&atypes, opts, ir, wi);
+ set_wall_atomtype(&atypes, opts, ir, wi, logger);
if (bRenum)
{
atypes.renumberTypes(interactions, &sys, ir->wall_atomtype, bVerbose);
if (bVerbose)
{
- fprintf(stderr, "converting bonded parameters...\n");
+ GMX_LOG(logger.info).asParagraph().appendTextFormatted("converting bonded parameters...");
}
const int ntype = atypes.size();
/* check masses */
check_mol(&sys, wi);
- checkForUnboundAtoms(&sys, bVerbose, wi);
+ checkForUnboundAtoms(&sys, bVerbose, wi, logger);
if (EI_DYNAMICS(ir->eI) && ir->eI != eiBD)
{
if (bVerbose)
{
- fprintf(stderr, "initialising group options...\n");
+ GMX_LOG(logger.info).asParagraph().appendTextFormatted("initialising group options...");
}
do_index(mdparin, ftp2fn_null(efNDX, NFILE, fnm), &sys, bVerbose, mdModules.notifier(), ir, wi);
}
if (buffer_temp > 0)
{
- sprintf(warn_buf,
+ std::string warningMessage = gmx::formatString(
"NVE simulation: will use the initial temperature of %.3f K for "
"determining the Verlet buffer size",
buffer_temp);
- warning_note(wi, warn_buf);
+ warning_note(wi, warningMessage);
}
else
{
- sprintf(warn_buf,
+ std::string warningMessage = gmx::formatString(
"NVE simulation with an initial temperature of zero: will use a Verlet "
"buffer of %d%%. Check your energy drift!",
gmx::roundToInt(verlet_buffer_ratio_NVE_T0 * 100));
- warning_note(wi, warn_buf);
+ warning_note(wi, warningMessage);
}
}
else
if (ir->verletbuf_tol > 1.1 * driftTolerance * totalEnergyDriftPerAtomPerPicosecond)
{
- sprintf(warn_buf,
+ std::string warningMessage = gmx::formatString(
"You are using a Verlet buffer tolerance of %g kJ/mol/ps for an "
"NVE simulation of length %g ps, which can give a final drift of "
"%d%%. For conserving energy to %d%% when using constraints, you "
gmx::roundToInt(ir->verletbuf_tol / totalEnergyDriftPerAtomPerPicosecond * 100),
gmx::roundToInt(100 * driftTolerance),
driftTolerance * totalEnergyDriftPerAtomPerPicosecond);
- warning_note(wi, warn_buf);
+ warning_note(wi, warningMessage);
}
}
- set_verlet_buffer(&sys, ir, buffer_temp, state.box, wi);
+ set_verlet_buffer(&sys, ir, buffer_temp, state.box, wi, logger);
}
}
}
{
if (bVerbose)
{
- fprintf(stderr, "getting data from old trajectory ...\n");
+ GMX_LOG(logger.info)
+ .asParagraph()
+ .appendTextFormatted("getting data from old trajectory ...");
}
cont_status(ftp2fn(efTRN, NFILE, fnm), ftp2fn_null(efEDR, NFILE, fnm), bNeedVel, bGenVel,
- fr_time, ir, &state, &sys, oenv);
+ fr_time, ir, &state, &sys, oenv, logger);
}
if (ir->pbcType == PbcType::XY && ir->nwall != 2)
if (EEL_PME(ir->coulombtype))
{
float ratio = pme_load_estimate(sys, *ir, state.box);
- fprintf(stderr, "Estimate for the relative computational load of the PME mesh part: %.2f\n", ratio);
+ GMX_LOG(logger.info)
+ .asParagraph()
+ .appendTextFormatted(
+ "Estimate for the relative computational load of the PME mesh part: %.2f", ratio);
/* With free energy we might need to do PME both for the A and B state
* charges. This will double the cost, but the optimal performance will
* then probably be at a slightly larger cut-off and grid spacing.
}
{
- char warn_buf[STRLEN];
- double cio = compute_io(ir, sys.natoms, sys.groups, F_NRE, 1);
- sprintf(warn_buf, "This run will generate roughly %.0f Mb of data", cio);
+ double cio = compute_io(ir, sys.natoms, sys.groups, F_NRE, 1);
+ std::string warningMessage =
+ gmx::formatString("This run will generate roughly %.0f Mb of data", cio);
if (cio > 2000)
{
set_warning_line(wi, mdparin, -1);
- warning_note(wi, warn_buf);
+ warning_note(wi, warningMessage);
}
else
{
- printf("%s\n", warn_buf);
+ GMX_LOG(logger.info).asParagraph().appendText(warningMessage);
}
}
if (bVerbose)
{
- fprintf(stderr, "writing run input file...\n");
+ GMX_LOG(logger.info).asParagraph().appendTextFormatted("writing run input file...");
}
done_warning(wi, FARGS);
biod.pnpi.spb.ru / alexxy / gromacs.git / commitdiff