* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
* Copyright (c) 2013,2014,2015,2016,2017 by the GROMACS development team.
- * Copyright (c) 2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2018,2019,2020,2021, 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.
}
}
+static void print_runtime_info(t_inputrec* ir)
+{
+ char buf[STEPSTRSIZE];
+
+ printf(" Run start step %22s \n", gmx_step_str(ir->init_step, buf));
+ printf(" Run start time %22g ps \n", ir->init_step * ir->delta_t + ir->init_t);
+ printf(" Step to be made during run %22s \n", gmx_step_str(ir->nsteps, buf));
+ printf(" Runtime for the run %22g ps \n", ir->nsteps * ir->delta_t);
+ printf(" Run end step %22s \n", gmx_step_str(ir->init_step + ir->nsteps, buf));
+ printf(" Run end time %22g ps \n\n",
+ (ir->init_step + ir->nsteps) * ir->delta_t + ir->init_t);
+}
+
namespace gmx
{
.storeIsSet(&runToMaxTimeIsSet_)
.timeValue()
.description("Extend runtime until this ending time (ps)"));
- options->addOption(
- Int64Option("nsteps").store(&maxSteps_).storeIsSet(&maxStepsIsSet_).description("Change the number of steps"));
+ options->addOption(Int64Option("nsteps")
+ .store(&maxSteps_)
+ .storeIsSet(&maxStepsIsSet_)
+ .description("Change the number of steps remaining to be made"));
options->addOption(
BooleanOption("zeroq").store(&zeroQIsSet_).description("Set the charges of a group (from the index) to zero"));
}
gmx_mtop_t mtop;
t_atoms atoms;
t_state state;
- char buf[200], buf2[200];
+ char buf[STEPSTRSIZE];
+
+ if (static_cast<int>(extendTimeIsSet_) + static_cast<int>(maxStepsIsSet_) + static_cast<int>(runToMaxTimeIsSet_)
+ > 1)
+ {
+ printf("Multiple runtime modification operations cannot be done in a single call.\n");
+ return 1;
+ }
+
+ if ((extendTimeIsSet_ || maxStepsIsSet_ || runToMaxTimeIsSet_) && (zeroQIsSet_ || haveReadIndexFile_))
+ {
+ printf("Cannot do both runtime modification and charge-zeroing/index group extraction in a "
+ "single call.\n");
+ return 1;
+ }
+
+ if (zeroQIsSet_ && !haveReadIndexFile_)
+ {
+ printf("Charge zeroing need an index file.\n");
+ return 1;
+ }
- fprintf(stderr, "Reading toplogy and stuff from %s\n", inputTprFileName_.c_str());
t_inputrec irInstance;
t_inputrec* ir = &irInstance;
read_tpx_state(inputTprFileName_.c_str(), ir, &state, &mtop);
- int64_t currentMaxStep = ir->init_step;
- double currentRunTime = ir->init_step * ir->delta_t + ir->init_t;
- real currentMaxRunTime = 0.0;
- if (maxStepsIsSet_)
- {
- fprintf(stderr, "Setting nsteps to %s\n", gmx_step_str(maxSteps_, buf));
- ir->nsteps = maxSteps_;
- }
- else
+
+ if (extendTimeIsSet_ || maxStepsIsSet_ || runToMaxTimeIsSet_)
{
- /* Determine total number of steps remaining */
- if (extendTimeIsSet_)
- {
- ir->nsteps = ir->nsteps - (currentMaxStep - ir->init_step)
- + gmx::roundToInt64(extendTime_ / ir->delta_t);
- printf("Extending remaining runtime of by %g ps (now %s steps)\n", extendTime_,
- gmx_step_str(ir->nsteps, buf));
- }
- else if (runToMaxTimeIsSet_)
+ // Doing runtime modification
+
+ const double inputTimeAtStartOfRun = ir->init_step * ir->delta_t + ir->init_t;
+ const int64_t inputStepAtEndOfRun = ir->init_step + ir->nsteps;
+ const double inputTimeAtEndOfRun = inputStepAtEndOfRun * ir->delta_t + ir->init_t;
+
+ printf("Input file:\n");
+ print_runtime_info(ir);
+
+ if (maxStepsIsSet_)
{
- printf("nsteps = %s, run_step = %s, current_t = %g, until = %g\n",
- gmx_step_str(ir->nsteps, buf), gmx_step_str(currentMaxStep, buf2),
- currentRunTime, runToMaxTime_);
- ir->nsteps = gmx::roundToInt64((currentMaxRunTime - currentRunTime) / ir->delta_t);
- printf("Extending remaining runtime until %g ps (now %s steps)\n", currentMaxRunTime,
- gmx_step_str(ir->nsteps, buf));
+ fprintf(stderr, "Setting nsteps to %s\n", gmx_step_str(maxSteps_, buf));
+ ir->nsteps = maxSteps_;
}
- else
+ else if (extendTimeIsSet_)
{
- ir->nsteps -= currentMaxStep - ir->init_step;
- /* Print message */
- printf("%s steps (%g ps) remaining from first run.\n", gmx_step_str(ir->nsteps, buf),
- ir->nsteps * ir->delta_t);
+ printf("Extending remaining runtime by %g ps\n", extendTime_);
+ ir->nsteps += gmx::roundToInt64(extendTime_ / ir->delta_t);
}
- }
-
- if (maxStepsIsSet_ || zeroQIsSet_ || (ir->nsteps > 0))
- {
- ir->init_step = currentMaxStep;
-
- if (haveReadIndexFile_ || !(maxStepsIsSet_ || extendTimeIsSet_ || runToMaxTimeIsSet_))
+ else if (runToMaxTimeIsSet_)
{
- atoms = gmx_mtop_global_atoms(&mtop);
- int gnx = 0;
- int* index = nullptr;
- char* grpname = nullptr;
- get_index(&atoms, inputIndexFileName_.c_str(), 1, &gnx, &index, &grpname);
- bool bSel = false;
- if (!zeroQIsSet_)
+ if (runToMaxTime_ <= inputTimeAtStartOfRun)
{
- bSel = (gnx != state.natoms);
- for (int i = 0; ((i < gnx) && (!bSel)); i++)
- {
- bSel = (i != index[i]);
- }
+ printf("The requested run end time is at/before the run start time.\n");
+ return 1;
}
- else
+ if (runToMaxTime_ < inputTimeAtEndOfRun)
{
- bSel = false;
- }
- if (bSel)
- {
- fprintf(stderr,
- "Will write subset %s of original tpx containing %d "
- "atoms\n",
- grpname, gnx);
- reduce_topology_x(gnx, index, &mtop, state.x.rvec_array(), state.v.rvec_array());
- state.natoms = gnx;
- }
- else if (zeroQIsSet_)
- {
- zeroq(index, &mtop);
- fprintf(stderr, "Zero-ing charges for group %s\n", grpname);
+ printf("The requested run end time is before the original run end time.\n");
+ printf("Reducing remaining runtime to %g ps\n", runToMaxTime_);
}
else
{
- fprintf(stderr, "Will write full tpx file (no selection)\n");
+ printf("Extending remaining runtime to %g ps\n", runToMaxTime_);
}
+ ir->nsteps = gmx::roundToInt64((runToMaxTime_ - inputTimeAtStartOfRun) / ir->delta_t);
}
- double stateTime = ir->init_t + ir->init_step * ir->delta_t;
- sprintf(buf, "Writing statusfile with starting step %s%s and length %s%s steps...\n", "%10",
- PRId64, "%10", PRId64);
- fprintf(stderr, buf, ir->init_step, ir->nsteps);
- fprintf(stderr, " time %10.3f and length %10.3f ps\n",
- stateTime, ir->nsteps * ir->delta_t);
- write_tpx_state(outputTprFileName_.c_str(), ir, &state, &mtop);
+ printf("\nOutput file:\n");
+ print_runtime_info(ir);
}
else
{
- printf("You've simulated long enough. Not writing tpr file\n");
+ // If zeroQIsSet_, then we are doing charge zero-ing; otherwise index group extraction
+ // In both cases an index filename has been provided
+
+ atoms = gmx_mtop_global_atoms(&mtop);
+ int gnx = 0;
+ int* index = nullptr;
+ char* grpname = nullptr;
+ get_index(&atoms, inputIndexFileName_.c_str(), 1, &gnx, &index, &grpname);
+ bool bSel = false;
+ if (!zeroQIsSet_)
+ {
+ bSel = (gnx != state.natoms);
+ for (int i = 0; ((i < gnx) && (!bSel)); i++)
+ {
+ bSel = (i != index[i]);
+ }
+ }
+ else
+ {
+ bSel = false;
+ }
+ if (bSel)
+ {
+ fprintf(stderr,
+ "Will write subset %s of original tpx containing %d "
+ "atoms\n",
+ grpname, gnx);
+ reduce_topology_x(gnx, index, &mtop, state.x.rvec_array(), state.v.rvec_array());
+ state.natoms = gnx;
+ }
+ else if (zeroQIsSet_)
+ {
+ zeroq(index, &mtop);
+ fprintf(stderr, "Zero-ing charges for group %s\n", grpname);
+ }
+ else
+ {
+ fprintf(stderr, "Will write full tpx file (no selection)\n");
+ }
}
+ // Writing output tpx regardless of the operation performed
+ write_tpx_state(outputTprFileName_.c_str(), ir, &state, &mtop);
+
return 0;
}
biod.pnpi.spb.ru / alexxy / gromacs.git / commitdiff