void affine_start_split(affine_stack_t **p) {
if((*p)->trivial_par) {
free_pars(*p);
(*p)->par_next = malloc(sizeof(affine_par_t));
init_par((*p)->par_next);
(*p)->par_cur = (*p)->par_next;
(*p)->trivial_par =false;
} else {
affine_par_t** par_iter = &((*p)->par_next);
while((*par_iter)!=NULL) par_iter=&((*par_iter)->par_next);
(*par_iter) = malloc(sizeof(affine_par_t));
(*p)->par_cur = (*par_iter);
init_par(*par_iter);
if((*p)->prev == NULL || (*p)->prev->par_next == NULL) {
(*par_iter)->cur = (*p)->cur;
}
}
}
int main(int argc, char **argv) {
/* Data */
int p, n, niter;
DATA data; /* all data */
PAR par;
char newName[256];
const gsl_rng_type *T;
gsl_rng *r;
gsl_rng_env_setup();
T = gsl_rng_default;
r = gsl_rng_alloc(T);
if (!(argc == 2 || argc == 4)) {
fprintf(stderr, "usage: msblender [data] [ncompPos] [ncompNeg]\n");
fprintf(stderr, "usage: msblender [data] (default: ncompPos=2, ncompNeg=2)\n");
return 1;
}
FILE *fp = fopen(argv[1], "r");
if(fp == NULL) {
fprintf(stderr, "Data file %s does not exist.\n", argv[1]);
return 1;
}
if(argc >= 3) par.ncomp = atoi(argv[2]);
else par.ncomp = 2;
if(argc >= 4) par.ncomp0 = atoi(argv[3]);
else par.ncomp0 = 2;
niter = 30;
p = nrow(fp) - 1;
rewind(fp);
n = ncol(fp) - 1;
rewind(fp);
/* Read complete data */
read_data(fp, &data, &p, &n);
alloc_par(&par, &data);
init_par(&par, &data, r);
/* Estimation */
mvEM(&par, &data, niter, r);
/* Output */
strcpy(newName, argv[1]);
strcat(newName, ".msblender_out");
FILE *fpout = fopen(newName, "w");
writeResult(fpout, &par, &data);
free_data(&data);
fclose(fp);
fclose(fpout);
return 0;
}
int main(int argc, char *argv[])
{
t_commrec *cr;
t_bin *rb;
double *r;
rvec *v;
int k, i, ni, mi, n, m;
cr = init_par(&argc, argv);
n = strtol(argv[1], NULL, 10);
m = strtol(argv[2], NULL, 10);
fprintf(stdlog, "n=%d\n", n);
rb = mk_bin();
snew(r, n);
snew(v, m);
for (k = 0; (k < 3); k++)
{
fprintf(stdlog, "\nk=%d\n", k);
reset_bin(rb);
for (i = 0; (i < n); i++)
{
r[i] = i+k;
}
for (i = 0; (i < m); i++)
{
v[i][XX] = 4*i+k;
v[i][YY] = 4*i+k+1;
v[i][ZZ] = 4*i+k+2;
}
ni = add_bind(stdlog, rb, n, r);
mi = add_binr(stdlog, rb, DIM*m, v[0]);
sum_bin(rb, cr);
extract_bind(rb, ni, n, r);
extract_binr(rb, mi, DIM*m, v[0]);
for (i = 0; (i < n); i++)
{
fprintf(stdlog, "r[%d] = %e\n", i, r[i]);
}
for (i = 0; (i < m); i++)
{
fprintf(stdlog, "v[%d] = (%e,%e,%e)\n", i, v[i][XX], v[i][YY], v[i][ZZ]);
}
}
fflush(stdlog);
return 0;
}
int main(int argc, char **argv) {
/* Data */
int p, n;
DATA data; /* all data */
PAR par;
char newName[256];
const gsl_rng_type *T;
gsl_rng *r;
gsl_rng_env_setup();
T = gsl_rng_default;
r = gsl_rng_alloc(T);
if (argc != 2) {
fprintf(stderr, "usage: agreementScore [data]\n");
return 1;
}
FILE *fp = fopen(argv[1], "r");
if(fp == NULL) {
fprintf(stderr, "Data file %s does not exist.\n", argv[1]);
return 1;
}
p = nrow(fp) - 1;
rewind(fp);
n = ncol(fp) - 1;
rewind(fp);
/* Read complete data */
read_data(fp, &data, &p, &n);
init_par(&par, &data, r);
/* Estimation */
agreeScore(&par, &data, r);
/* Output */
strcpy(newName, argv[1]);
strcat(newName, "_agreement");
FILE *fpout = fopen(newName, "w");
writeResult(fpout, &par, &data);
free_data(&data);
fclose(fp);
fclose(fpout);
return 0;
}
void affine_save(affine_stack_t **p) {
affine_stack_t *old = *p;
*p = malloc(sizeof(affine_stack_t));
(*p)->cur = old->cur;
(*p)->prev = old;
(*p)->par_cur = NULL;
if(old->par_next != NULL) {
(*p)->par_next = malloc(sizeof(affine_par_t));
init_par((*p)->par_next);
(*p)->trivial_par = true;
} else {
(*p)->par_next = NULL;
(*p)->trivial_par = false;
}
}
int main(int argc,char *argv[])
{
const char *desc[] = {
#ifdef GMX_OPENMM
"This is an experimental release of GROMACS for accelerated",
"Molecular Dynamics simulations on GPU processors. Support is provided",
"by the OpenMM library (https://simtk.org/home/openmm).[PAR]",
"*Warning*[BR]",
"This release is targeted at developers and advanced users and",
"care should be taken before production use. The following should be",
"noted before using the program:[PAR]",
" * The current release runs only on modern nVidia GPU hardware with CUDA support.",
"Make sure that the necessary CUDA drivers and libraries for your operating system",
"are already installed. The CUDA SDK also should be installed in order to compile",
"the program from source (http://www.nvidia.com/object/cuda_home.html).[PAR]",
" * Multiple GPU cards are not supported.[PAR]",
" * Only a small subset of the GROMACS features and options are supported on the GPUs.",
"See below for a detailed list.[PAR]",
" * Consumer level GPU cards are known to often have problems with faulty memory.",
"It is recommended that a full memory check of the cards is done at least once",
"(for example, using the memtest=full option).",
"A partial memory check (for example, memtest=15) before and",
"after the simulation run would help spot",
"problems resulting from processor overheating.[PAR]",
" * The maximum size of the simulated systems depends on the available",
"GPU memory,for example, a GTX280 with 1GB memory has been tested with systems",
"of up to about 100,000 atoms.[PAR]",
" * In order to take a full advantage of the GPU platform features, many algorithms",
"have been implemented in a very different way than they are on the CPUs.",
"Therefore numercal correspondence between properties of the state of",
"simulated systems should not be expected. Moreover, the values will likely vary",
"when simulations are done on different GPU hardware.[PAR]",
" * Frequent retrieval of system state information such as",
"trajectory coordinates and energies can greatly influence the performance",
"of the program due to slow CPU<->GPU memory transfer speed.[PAR]",
" * MD algorithms are complex, and although the Gromacs code is highly tuned for them,",
"they often do not translate very well onto the streaming architetures.",
"Realistic expectations about the achievable speed-up from test with GTX280:",
"For small protein systems in implicit solvent using all-vs-all kernels the acceleration",
"can be as high as 20 times, but in most other setups involving cutoffs and PME the",
"acceleration is usually only ~4 times relative to a 3GHz CPU.[PAR]",
"Supported features:[PAR]",
" * Integrators: md/md-vv/md-vv-avek, sd/sd1 and bd.\n",
" * Long-range interactions (option coulombtype): Reaction-Field, Ewald, PME, and cut-off (for Implicit Solvent only)\n",
" * Temperature control: Supported only with the md/md-vv/md-vv-avek, sd/sd1 and bd integrators.\n",
" * Pressure control: Supported.\n",
" * Implicit solvent: Supported.\n",
"A detailed description can be found on the GROMACS website:\n",
"http://www.gromacs.org/gpu[PAR]",
/* From the original mdrun documentaion */
"The [TT]mdrun[tt] program reads the run input file ([TT]-s[tt])",
"and distributes the topology over nodes if needed.",
"[TT]mdrun[tt] produces at least four output files.",
"A single log file ([TT]-g[tt]) is written, unless the option",
"[TT]-seppot[tt] is used, in which case each node writes a log file.",
"The trajectory file ([TT]-o[tt]), contains coordinates, velocities and",
"optionally forces.",
"The structure file ([TT]-c[tt]) contains the coordinates and",
"velocities of the last step.",
"The energy file ([TT]-e[tt]) contains energies, the temperature,",
"pressure, etc, a lot of these things are also printed in the log file.",
"Optionally coordinates can be written to a compressed trajectory file",
"([TT]-x[tt]).[PAR]",
/* openmm specific information */
"Usage with OpenMM:[BR]",
"[TT]mdrun -device \"OpenMM:platform=Cuda,memtest=15,deviceid=0,force-device=no\"[tt][PAR]",
"Options:[PAR]",
" [TT]platform[tt] = Cuda\t\t:\tThe only available value. OpenCL support will be available in future.\n",
" [TT]memtest[tt] = 15\t\t:\tRun a partial, random GPU memory test for the given amount of seconds. A full test",
"(recommended!) can be run with \"memtest=full\". Memory testing can be disabled with \"memtest=off\".\n",
" [TT]deviceid[tt] = 0\t\t:\tSpecify the target device when multiple cards are present.",
"Only one card can be used at any given time though.\n",
" [TT]force-device[tt] = no\t\t:\tIf set to \"yes\" [TT]mdrun[tt] will be forced to execute on",
"hardware that is not officially supported. GPU acceleration can also be achieved on older",
"but Cuda capable cards, although the simulation might be too slow, and the memory limits too strict.",
#else
"The [TT]mdrun[tt] program is the main computational chemistry engine",
"within GROMACS. Obviously, it performs Molecular Dynamics simulations,",
"but it can also perform Stochastic Dynamics, Energy Minimization,",
"test particle insertion or (re)calculation of energies.",
"Normal mode analysis is another option. In this case [TT]mdrun[tt]",
"builds a Hessian matrix from single conformation.",
"For usual Normal Modes-like calculations, make sure that",
"the structure provided is properly energy-minimized.",
"The generated matrix can be diagonalized by [TT]g_nmeig[tt].[PAR]",
"The [TT]mdrun[tt] program reads the run input file ([TT]-s[tt])",
"and distributes the topology over nodes if needed.",
"[TT]mdrun[tt] produces at least four output files.",
"A single log file ([TT]-g[tt]) is written, unless the option",
"[TT]-seppot[tt] is used, in which case each node writes a log file.",
"The trajectory file ([TT]-o[tt]), contains coordinates, velocities and",
"optionally forces.",
"The structure file ([TT]-c[tt]) contains the coordinates and",
"velocities of the last step.",
"The energy file ([TT]-e[tt]) contains energies, the temperature,",
"pressure, etc, a lot of these things are also printed in the log file.",
"Optionally coordinates can be written to a compressed trajectory file",
"([TT]-x[tt]).[PAR]",
"The option [TT]-dhdl[tt] is only used when free energy calculation is",
"turned on.[PAR]",
"When [TT]mdrun[tt] is started using MPI with more than 1 node, parallelization",
"is used. By default domain decomposition is used, unless the [TT]-pd[tt]",
"option is set, which selects particle decomposition.[PAR]",
"With domain decomposition, the spatial decomposition can be set",
"with option [TT]-dd[tt]. By default [TT]mdrun[tt] selects a good decomposition.",
"The user only needs to change this when the system is very inhomogeneous.",
"Dynamic load balancing is set with the option [TT]-dlb[tt],",
"which can give a significant performance improvement,",
"especially for inhomogeneous systems. The only disadvantage of",
"dynamic load balancing is that runs are no longer binary reproducible,",
"but in most cases this is not important.",
"By default the dynamic load balancing is automatically turned on",
"when the measured performance loss due to load imbalance is 5% or more.",
"At low parallelization these are the only important options",
"for domain decomposition.",
"At high parallelization the options in the next two sections",
"could be important for increasing the performace.",
"[PAR]",
"When PME is used with domain decomposition, separate nodes can",
"be assigned to do only the PME mesh calculation;",
"this is computationally more efficient starting at about 12 nodes.",
"The number of PME nodes is set with option [TT]-npme[tt],",
"this can not be more than half of the nodes.",
"By default [TT]mdrun[tt] makes a guess for the number of PME",
"nodes when the number of nodes is larger than 11 or performance wise",
"not compatible with the PME grid x dimension.",
"But the user should optimize npme. Performance statistics on this issue",
"are written at the end of the log file.",
"For good load balancing at high parallelization, the PME grid x and y",
"dimensions should be divisible by the number of PME nodes",
"(the simulation will run correctly also when this is not the case).",
"[PAR]",
"This section lists all options that affect the domain decomposition.",
"[PAR]",
"Option [TT]-rdd[tt] can be used to set the required maximum distance",
"for inter charge-group bonded interactions.",
"Communication for two-body bonded interactions below the non-bonded",
"cut-off distance always comes for free with the non-bonded communication.",
"Atoms beyond the non-bonded cut-off are only communicated when they have",
"missing bonded interactions; this means that the extra cost is minor",
"and nearly indepedent of the value of [TT]-rdd[tt].",
"With dynamic load balancing option [TT]-rdd[tt] also sets",
"the lower limit for the domain decomposition cell sizes.",
"By default [TT]-rdd[tt] is determined by [TT]mdrun[tt] based on",
"the initial coordinates. The chosen value will be a balance",
"between interaction range and communication cost.",
"[PAR]",
"When inter charge-group bonded interactions are beyond",
"the bonded cut-off distance, [TT]mdrun[tt] terminates with an error message.",
"For pair interactions and tabulated bonds",
"that do not generate exclusions, this check can be turned off",
"with the option [TT]-noddcheck[tt].",
"[PAR]",
"When constraints are present, option [TT]-rcon[tt] influences",
"the cell size limit as well.",
"Atoms connected by NC constraints, where NC is the LINCS order plus 1,",
"should not be beyond the smallest cell size. A error message is",
"generated when this happens and the user should change the decomposition",
"or decrease the LINCS order and increase the number of LINCS iterations.",
"By default [TT]mdrun[tt] estimates the minimum cell size required for P-LINCS",
"in a conservative fashion. For high parallelization it can be useful",
"to set the distance required for P-LINCS with the option [TT]-rcon[tt].",
"[PAR]",
"The [TT]-dds[tt] option sets the minimum allowed x, y and/or z scaling",
"of the cells with dynamic load balancing. [TT]mdrun[tt] will ensure that",
"the cells can scale down by at least this factor. This option is used",
"for the automated spatial decomposition (when not using [TT]-dd[tt])",
"as well as for determining the number of grid pulses, which in turn",
"sets the minimum allowed cell size. Under certain circumstances",
"the value of [TT]-dds[tt] might need to be adjusted to account for",
"high or low spatial inhomogeneity of the system.",
"[PAR]",
"The option [TT]-gcom[tt] can be used to only do global communication",
"every n steps.",
"This can improve performance for highly parallel simulations",
"where this global communication step becomes the bottleneck.",
"For a global thermostat and/or barostat the temperature",
"and/or pressure will also only be updated every [TT]-gcom[tt] steps.",
"By default it is set to the minimum of nstcalcenergy and nstlist.[PAR]",
"With [TT]-rerun[tt] an input trajectory can be given for which ",
"forces and energies will be (re)calculated. Neighbor searching will be",
"performed for every frame, unless [TT]nstlist[tt] is zero",
"(see the [TT].mdp[tt] file).[PAR]",
"ED (essential dynamics) sampling is switched on by using the [TT]-ei[tt]",
"flag followed by an [TT].edi[tt] file.",
"The [TT].edi[tt] file can be produced using options in the essdyn",
"menu of the WHAT IF program. [TT]mdrun[tt] produces a [TT].edo[tt] file that",
"contains projections of positions, velocities and forces onto selected",
"eigenvectors.[PAR]",
"When user-defined potential functions have been selected in the",
"[TT].mdp[tt] file the [TT]-table[tt] option is used to pass [TT]mdrun[tt]",
"a formatted table with potential functions. The file is read from",
"either the current directory or from the [TT]GMXLIB[tt] directory.",
"A number of pre-formatted tables are presented in the [TT]GMXLIB[tt] dir,",
"for 6-8, 6-9, 6-10, 6-11, 6-12 Lennard-Jones potentials with",
"normal Coulomb.",
"When pair interactions are present, a separate table for pair interaction",
"functions is read using the [TT]-tablep[tt] option.[PAR]",
"When tabulated bonded functions are present in the topology,",
"interaction functions are read using the [TT]-tableb[tt] option.",
"For each different tabulated interaction type the table file name is",
"modified in a different way: before the file extension an underscore is",
"appended, then a 'b' for bonds, an 'a' for angles or a 'd' for dihedrals",
"and finally the table number of the interaction type.[PAR]",
"The options [TT]-px[tt] and [TT]-pf[tt] are used for writing pull COM",
"coordinates and forces when pulling is selected",
"in the [TT].mdp[tt] file.[PAR]",
"With [TT]-multi[tt] or [TT]-multidir[tt], multiple systems can be ",
"simulated in parallel.",
"As many input files/directories are required as the number of systems. ",
"The [TT]-multidir[tt] option takes a list of directories (one for each ",
"system) and runs in each of them, using the input/output file names, ",
"such as specified by e.g. the [TT]-s[tt] option, relative to these ",
"directories.",
"With [TT]-multi[tt], the system number is appended to the run input ",
"and each output filename, for instance [TT]topol.tpr[tt] becomes",
"[TT]topol0.tpr[tt], [TT]topol1.tpr[tt] etc.",
"The number of nodes per system is the total number of nodes",
"divided by the number of systems.",
"One use of this option is for NMR refinement: when distance",
"or orientation restraints are present these can be ensemble averaged",
"over all the systems.[PAR]",
"With [TT]-replex[tt] replica exchange is attempted every given number",
"of steps. The number of replicas is set with the [TT]-multi[tt] or ",
"[TT]-multidir[tt] option, described above.",
"All run input files should use a different coupling temperature,",
"the order of the files is not important. The random seed is set with",
"[TT]-reseed[tt]. The velocities are scaled and neighbor searching",
"is performed after every exchange.[PAR]",
"Finally some experimental algorithms can be tested when the",
"appropriate options have been given. Currently under",
"investigation are: polarizability and X-ray bombardments.",
"[PAR]",
"The option [TT]-pforce[tt] is useful when you suspect a simulation",
"crashes due to too large forces. With this option coordinates and",
"forces of atoms with a force larger than a certain value will",
"be printed to stderr.",
"[PAR]",
"Checkpoints containing the complete state of the system are written",
"at regular intervals (option [TT]-cpt[tt]) to the file [TT]-cpo[tt],",
"unless option [TT]-cpt[tt] is set to -1.",
"The previous checkpoint is backed up to [TT]state_prev.cpt[tt] to",
"make sure that a recent state of the system is always available,",
"even when the simulation is terminated while writing a checkpoint.",
"With [TT]-cpnum[tt] all checkpoint files are kept and appended",
"with the step number.",
"A simulation can be continued by reading the full state from file",
"with option [TT]-cpi[tt]. This option is intelligent in the way that",
"if no checkpoint file is found, Gromacs just assumes a normal run and",
"starts from the first step of the [TT].tpr[tt] file. By default the output",
"will be appending to the existing output files. The checkpoint file",
"contains checksums of all output files, such that you will never",
"loose data when some output files are modified, corrupt or removed.",
"There are three scenarios with [TT]-cpi[tt]:[PAR]",
"[TT]*[tt] no files with matching names are present: new output files are written[PAR]",
"[TT]*[tt] all files are present with names and checksums matching those stored",
"in the checkpoint file: files are appended[PAR]",
"[TT]*[tt] otherwise no files are modified and a fatal error is generated[PAR]",
"With [TT]-noappend[tt] new output files are opened and the simulation",
"part number is added to all output file names.",
"Note that in all cases the checkpoint file itself is not renamed",
"and will be overwritten, unless its name does not match",
"the [TT]-cpo[tt] option.",
"[PAR]",
"With checkpointing the output is appended to previously written",
"output files, unless [TT]-noappend[tt] is used or none of the previous",
"output files are present (except for the checkpoint file).",
"The integrity of the files to be appended is verified using checksums",
"which are stored in the checkpoint file. This ensures that output can",
"not be mixed up or corrupted due to file appending. When only some",
"of the previous output files are present, a fatal error is generated",
"and no old output files are modified and no new output files are opened.",
"The result with appending will be the same as from a single run.",
"The contents will be binary identical, unless you use a different number",
"of nodes or dynamic load balancing or the FFT library uses optimizations",
"through timing.",
"[PAR]",
"With option [TT]-maxh[tt] a simulation is terminated and a checkpoint",
"file is written at the first neighbor search step where the run time",
"exceeds [TT]-maxh[tt]*0.99 hours.",
"[PAR]",
"When [TT]mdrun[tt] receives a TERM signal, it will set nsteps to the current",
"step plus one. When [TT]mdrun[tt] receives an INT signal (e.g. when ctrl+C is",
"pressed), it will stop after the next neighbor search step ",
"(with nstlist=0 at the next step).",
"In both cases all the usual output will be written to file.",
"When running with MPI, a signal to one of the [TT]mdrun[tt] processes",
"is sufficient, this signal should not be sent to mpirun or",
"the [TT]mdrun[tt] process that is the parent of the others.",
"[PAR]",
"When [TT]mdrun[tt] is started with MPI, it does not run niced by default."
#endif
};
t_commrec *cr;
t_filenm fnm[] = {
{ efTPX, NULL, NULL, ffREAD },
{ efTRN, "-o", NULL, ffWRITE },
{ efXTC, "-x", NULL, ffOPTWR },
{ efCPT, "-cpi", NULL, ffOPTRD },
{ efCPT, "-cpo", NULL, ffOPTWR },
{ efSTO, "-c", "confout", ffWRITE },
{ efEDR, "-e", "ener", ffWRITE },
{ efLOG, "-g", "md", ffWRITE },
{ efXVG, "-dhdl", "dhdl", ffOPTWR },
{ efXVG, "-field", "field", ffOPTWR },
{ efXVG, "-table", "table", ffOPTRD },
{ efXVG, "-tabletf", "tabletf", ffOPTRD },
{ efXVG, "-tablep", "tablep", ffOPTRD },
{ efXVG, "-tableb", "table", ffOPTRD },
{ efTRX, "-rerun", "rerun", ffOPTRD },
{ efXVG, "-tpi", "tpi", ffOPTWR },
{ efXVG, "-tpid", "tpidist", ffOPTWR },
{ efEDI, "-ei", "sam", ffOPTRD },
{ efEDO, "-eo", "sam", ffOPTWR },
{ efGCT, "-j", "wham", ffOPTRD },
{ efGCT, "-jo", "bam", ffOPTWR },
{ efXVG, "-ffout", "gct", ffOPTWR },
{ efXVG, "-devout", "deviatie", ffOPTWR },
{ efXVG, "-runav", "runaver", ffOPTWR },
{ efXVG, "-px", "pullx", ffOPTWR },
{ efXVG, "-pf", "pullf", ffOPTWR },
{ efXVG, "-ro", "rotation", ffOPTWR },
{ efLOG, "-ra", "rotangles",ffOPTWR },
{ efLOG, "-rs", "rotslabs", ffOPTWR },
{ efLOG, "-rt", "rottorque",ffOPTWR },
{ efMTX, "-mtx", "nm", ffOPTWR },
{ efNDX, "-dn", "dipole", ffOPTWR },
{ efRND, "-multidir",NULL, ffOPTRDMULT},
{ efGMX, "-mmcg", "mmcg", ffOPTRD },
{ efWPO, "-wpot", "wpot", ffOPTRD }
};
#define NFILE asize(fnm)
/* Command line options ! */
gmx_bool bCart = FALSE;
gmx_bool bPPPME = FALSE;
gmx_bool bPartDec = FALSE;
gmx_bool bDDBondCheck = TRUE;
gmx_bool bDDBondComm = TRUE;
gmx_bool bVerbose = FALSE;
gmx_bool bCompact = TRUE;
gmx_bool bSepPot = FALSE;
gmx_bool bRerunVSite = FALSE;
gmx_bool bIonize = FALSE;
gmx_bool bConfout = TRUE;
gmx_bool bReproducible = FALSE;
int npme=-1;
int nmultisim=0;
int nstglobalcomm=-1;
int repl_ex_nst=0;
int repl_ex_seed=-1;
int nstepout=100;
int nthreads=0; /* set to determine # of threads automatically */
int resetstep=-1;
rvec realddxyz={0,0,0};
const char *ddno_opt[ddnoNR+1] =
{ NULL, "interleave", "pp_pme", "cartesian", NULL };
const char *dddlb_opt[] =
{ NULL, "auto", "no", "yes", NULL };
real rdd=0.0,rconstr=0.0,dlb_scale=0.8,pforce=-1;
char *ddcsx=NULL,*ddcsy=NULL,*ddcsz=NULL;
real cpt_period=15.0,max_hours=-1;
gmx_bool bAppendFiles=TRUE;
gmx_bool bKeepAndNumCPT=FALSE;
gmx_bool bResetCountersHalfWay=FALSE;
output_env_t oenv=NULL;
const char *deviceOptions = "";
t_pargs pa[] = {
{ "-pd", FALSE, etBOOL,{&bPartDec},
"Use particle decompostion" },
{ "-dd", FALSE, etRVEC,{&realddxyz},
"Domain decomposition grid, 0 is optimize" },
#ifdef GMX_THREADS
{ "-nt", FALSE, etINT, {&nthreads},
"Number of threads to start (0 is guess)" },
#endif
{ "-npme", FALSE, etINT, {&npme},
"Number of separate nodes to be used for PME, -1 is guess" },
{ "-ddorder", FALSE, etENUM, {ddno_opt},
"DD node order" },
{ "-ddcheck", FALSE, etBOOL, {&bDDBondCheck},
"Check for all bonded interactions with DD" },
{ "-ddbondcomm", FALSE, etBOOL, {&bDDBondComm},
"HIDDENUse special bonded atom communication when [TT]-rdd[tt] > cut-off" },
{ "-rdd", FALSE, etREAL, {&rdd},
"The maximum distance for bonded interactions with DD (nm), 0 is determine from initial coordinates" },
{ "-rcon", FALSE, etREAL, {&rconstr},
"Maximum distance for P-LINCS (nm), 0 is estimate" },
{ "-dlb", FALSE, etENUM, {dddlb_opt},
"Dynamic load balancing (with DD)" },
{ "-dds", FALSE, etREAL, {&dlb_scale},
"Minimum allowed dlb scaling of the DD cell size" },
{ "-ddcsx", FALSE, etSTR, {&ddcsx},
"HIDDENThe DD cell sizes in x" },
{ "-ddcsy", FALSE, etSTR, {&ddcsy},
"HIDDENThe DD cell sizes in y" },
{ "-ddcsz", FALSE, etSTR, {&ddcsz},
"HIDDENThe DD cell sizes in z" },
{ "-gcom", FALSE, etINT,{&nstglobalcomm},
"Global communication frequency" },
{ "-v", FALSE, etBOOL,{&bVerbose},
"Be loud and noisy" },
{ "-compact", FALSE, etBOOL,{&bCompact},
"Write a compact log file" },
{ "-seppot", FALSE, etBOOL, {&bSepPot},
"Write separate V and dVdl terms for each interaction type and node to the log file(s)" },
{ "-pforce", FALSE, etREAL, {&pforce},
"Print all forces larger than this (kJ/mol nm)" },
{ "-reprod", FALSE, etBOOL,{&bReproducible},
"Try to avoid optimizations that affect binary reproducibility" },
{ "-cpt", FALSE, etREAL, {&cpt_period},
"Checkpoint interval (minutes)" },
{ "-cpnum", FALSE, etBOOL, {&bKeepAndNumCPT},
"Keep and number checkpoint files" },
{ "-append", FALSE, etBOOL, {&bAppendFiles},
"Append to previous output files when continuing from checkpoint instead of adding the simulation part number to all file names" },
{ "-maxh", FALSE, etREAL, {&max_hours},
"Terminate after 0.99 times this time (hours)" },
{ "-multi", FALSE, etINT,{&nmultisim},
"Do multiple simulations in parallel" },
{ "-replex", FALSE, etINT, {&repl_ex_nst},
"Attempt replica exchange every # steps" },
{ "-reseed", FALSE, etINT, {&repl_ex_seed},
"Seed for replica exchange, -1 is generate a seed" },
{ "-rerunvsite", FALSE, etBOOL, {&bRerunVSite},
"HIDDENRecalculate virtual site coordinates with [TT]-rerun[tt]" },
{ "-ionize", FALSE, etBOOL,{&bIonize},
"Do a simulation including the effect of an X-Ray bombardment on your system" },
{ "-confout", FALSE, etBOOL, {&bConfout},
"HIDDENWrite the last configuration with [TT]-c[tt] and force checkpointing at the last step" },
{ "-stepout", FALSE, etINT, {&nstepout},
"HIDDENFrequency of writing the remaining runtime" },
{ "-resetstep", FALSE, etINT, {&resetstep},
"HIDDENReset cycle counters after these many time steps" },
{ "-resethway", FALSE, etBOOL, {&bResetCountersHalfWay},
"HIDDENReset the cycle counters after half the number of steps or halfway [TT]-maxh[tt]" }
#ifdef GMX_OPENMM
,
{ "-device", FALSE, etSTR, {&deviceOptions},
"Device option string" }
#endif
};
gmx_edsam_t ed;
unsigned long Flags, PCA_Flags;
ivec ddxyz;
int dd_node_order;
gmx_bool bAddPart;
FILE *fplog,*fptest;
int sim_part,sim_part_fn;
const char *part_suffix=".part";
char suffix[STRLEN];
int rc;
char **multidir=NULL;
cr = init_par(&argc,&argv);
if (MASTER(cr))
CopyRight(stderr, argv[0]);
PCA_Flags = (PCA_KEEP_ARGS | PCA_NOEXIT_ON_ARGS | PCA_CAN_SET_DEFFNM
| (MASTER(cr) ? 0 : PCA_QUIET));
/* Comment this in to do fexist calls only on master
* works not with rerun or tables at the moment
* also comment out the version of init_forcerec in md.c
* with NULL instead of opt2fn
*/
/*
if (!MASTER(cr))
{
PCA_Flags |= PCA_NOT_READ_NODE;
}
*/
parse_common_args(&argc,argv,PCA_Flags, NFILE,fnm,asize(pa),pa,
asize(desc),desc,0,NULL, &oenv);
/* we set these early because they might be used in init_multisystem()
Note that there is the potential for npme>nnodes until the number of
threads is set later on, if there's thread parallelization. That shouldn't
lead to problems. */
dd_node_order = nenum(ddno_opt);
cr->npmenodes = npme;
#ifndef GMX_THREADS
nthreads=1;
#endif
/* now check the -multi and -multidir option */
if (opt2bSet("-multidir", NFILE, fnm))
{
int i;
if (nmultisim > 0)
{
gmx_fatal(FARGS, "mdrun -multi and -multidir options are mutually exclusive.");
}
nmultisim = opt2fns(&multidir, "-multidir", NFILE, fnm);
}
if (repl_ex_nst != 0 && nmultisim < 2)
gmx_fatal(FARGS,"Need at least two replicas for replica exchange (option -multi)");
if (nmultisim > 1) {
#ifndef GMX_THREADS
gmx_bool bParFn = (multidir == NULL);
init_multisystem(cr, nmultisim, multidir, NFILE, fnm, bParFn);
#else
gmx_fatal(FARGS,"mdrun -multi is not supported with the thread library.Please compile GROMACS with MPI support");
#endif
}
bAddPart = !bAppendFiles;
/* Check if there is ANY checkpoint file available */
sim_part = 1;
sim_part_fn = sim_part;
if (opt2bSet("-cpi",NFILE,fnm))
{
if (bSepPot && bAppendFiles)
{
gmx_fatal(FARGS,"Output file appending is not supported with -seppot");
}
bAppendFiles =
read_checkpoint_simulation_part(opt2fn_master("-cpi", NFILE,
fnm,cr),
&sim_part_fn,NULL,cr,
bAppendFiles,NFILE,fnm,
part_suffix,&bAddPart);
if (sim_part_fn==0 && MASTER(cr))
{
fprintf(stdout,"No previous checkpoint file present, assuming this is a new run.\n");
}
else
{
sim_part = sim_part_fn + 1;
}
if (MULTISIM(cr) && MASTER(cr))
{
check_multi_int(stdout,cr->ms,sim_part,"simulation part");
}
}
else
{
bAppendFiles = FALSE;
}
if (!bAppendFiles)
{
sim_part_fn = sim_part;
}
if (bAddPart)
{
/* Rename all output files (except checkpoint files) */
/* create new part name first (zero-filled) */
sprintf(suffix,"%s%04d",part_suffix,sim_part_fn);
add_suffix_to_output_names(fnm,NFILE,suffix);
if (MASTER(cr))
{
fprintf(stdout,"Checkpoint file is from part %d, new output files will be suffixed '%s'.\n",sim_part-1,suffix);
}
}
Flags = opt2bSet("-rerun",NFILE,fnm) ? MD_RERUN : 0;
Flags = Flags | (opt2bSet("-mmcg",NFILE,fnm) ? MD_MMCG : 0);
Flags = Flags | (bSepPot ? MD_SEPPOT : 0);
Flags = Flags | (bIonize ? MD_IONIZE : 0);
Flags = Flags | (bPartDec ? MD_PARTDEC : 0);
Flags = Flags | (bDDBondCheck ? MD_DDBONDCHECK : 0);
Flags = Flags | (bDDBondComm ? MD_DDBONDCOMM : 0);
Flags = Flags | (bConfout ? MD_CONFOUT : 0);
Flags = Flags | (bRerunVSite ? MD_RERUN_VSITE : 0);
Flags = Flags | (bReproducible ? MD_REPRODUCIBLE : 0);
Flags = Flags | (bAppendFiles ? MD_APPENDFILES : 0);
Flags = Flags | (bKeepAndNumCPT ? MD_KEEPANDNUMCPT : 0);
Flags = Flags | (sim_part>1 ? MD_STARTFROMCPT : 0);
Flags = Flags | (bResetCountersHalfWay ? MD_RESETCOUNTERSHALFWAY : 0);
Flags = Flags | (opt2bSet("-wpot",NFILE,fnm) ? MD_WALLPOT : 0);
/* We postpone opening the log file if we are appending, so we can
first truncate the old log file and append to the correct position
there instead. */
if ((MASTER(cr) || bSepPot) && !bAppendFiles)
{
gmx_log_open(ftp2fn(efLOG,NFILE,fnm),cr,!bSepPot,Flags,&fplog);
CopyRight(fplog,argv[0]);
please_cite(fplog,"Hess2008b");
please_cite(fplog,"Spoel2005a");
please_cite(fplog,"Lindahl2001a");
please_cite(fplog,"Berendsen95a");
}
else if (!MASTER(cr) && bSepPot)
{
gmx_log_open(ftp2fn(efLOG,NFILE,fnm),cr,!bSepPot,Flags,&fplog);
}
else
{
fplog = NULL;
}
ddxyz[XX] = (int)(realddxyz[XX] + 0.5);
ddxyz[YY] = (int)(realddxyz[YY] + 0.5);
ddxyz[ZZ] = (int)(realddxyz[ZZ] + 0.5);
rc = mdrunner(nthreads, fplog,cr,NFILE,fnm,oenv,bVerbose,bCompact,
nstglobalcomm, ddxyz,dd_node_order,rdd,rconstr,
dddlb_opt[0],dlb_scale,ddcsx,ddcsy,ddcsz,
nstepout,resetstep,nmultisim,repl_ex_nst,repl_ex_seed,
pforce, cpt_period,max_hours,deviceOptions,Flags);
if (gmx_parallel_env_initialized())
gmx_finalize();
if (MULTIMASTER(cr)) {
thanx(stderr);
}
/* Log file has to be closed in mdrunner if we are appending to it
(fplog not set here) */
if (MASTER(cr) && !bAppendFiles)
{
gmx_log_close(fplog);
}
return rc;
}
int gmx_pme_error(int argc,char *argv[])
{
const char *desc[] = {
"[TT]g_pme_error[tt] estimates the error of the electrostatic forces",
"if using the sPME algorithm. The flag [TT]-tune[tt] will determine",
"the splitting parameter such that the error is equally",
"distributed over the real and reciprocal space part.",
"The part of the error that stems from self interaction of the particles "
"is computationally demanding. However, a good a approximation is to",
"just use a fraction of the particles for this term which can be",
"indicated by the flag [TT]-self[tt].[PAR]",
};
real fs=0.0; /* 0 indicates: not set by the user */
real user_beta=-1.0;
real fracself=1.0;
t_inputinfo info;
t_state state; /* The state from the tpr input file */
gmx_mtop_t mtop; /* The topology from the tpr input file */
t_inputrec *ir=NULL; /* The inputrec from the tpr file */
FILE *fp=NULL;
t_commrec *cr;
unsigned long PCA_Flags;
gmx_bool bTUNE=FALSE;
gmx_bool bVerbose=FALSE;
int seed=0;
static t_filenm fnm[] = {
{ efTPX, "-s", NULL, ffREAD },
{ efOUT, "-o", "error", ffWRITE },
{ efTPX, "-so", "tuned", ffOPTWR }
};
output_env_t oenv=NULL;
t_pargs pa[] = {
{ "-beta", FALSE, etREAL, {&user_beta},
"If positive, overwrite ewald_beta from [TT].tpr[tt] file with this value" },
{ "-tune", FALSE, etBOOL, {&bTUNE},
"Tune the splitting parameter such that the error is equally distributed between real and reciprocal space" },
{ "-self", FALSE, etREAL, {&fracself},
"If between 0.0 and 1.0, determine self interaction error from just this fraction of the charged particles" },
{ "-seed", FALSE, etINT, {&seed},
"Random number seed used for Monte Carlo algorithm when [TT]-self[tt] is set to a value between 0.0 and 1.0" },
{ "-v", FALSE, etBOOL, {&bVerbose},
"Be loud and noisy" }
};
#define NFILE asize(fnm)
cr = init_par(&argc,&argv);
#ifdef GMX_LIB_MPI
MPI_Barrier(MPI_COMM_WORLD);
#endif
if (MASTER(cr))
CopyRight(stderr,argv[0]);
PCA_Flags = PCA_NOEXIT_ON_ARGS;
PCA_Flags |= (MASTER(cr) ? 0 : PCA_QUIET);
parse_common_args(&argc,argv,PCA_Flags,
NFILE,fnm,asize(pa),pa,asize(desc),desc,
0,NULL,&oenv);
if (!bTUNE)
bTUNE = opt2bSet("-so",NFILE,fnm);
info.n_entries = 1;
/* Allocate memory for the inputinfo struct: */
create_info(&info);
info.fourier_sp[0] = fs;
/* Read in the tpr file and open logfile for reading */
if (MASTER(cr))
{
snew(ir,1);
read_tpr_file(opt2fn("-s",NFILE,fnm), &info, &state, &mtop, ir, user_beta,fracself);
fp=fopen(opt2fn("-o",NFILE,fnm),"w");
}
/* Check consistency if the user provided fourierspacing */
if (fs > 0 && MASTER(cr))
{
/* Recalculate the grid dimensions using fourierspacing from user input */
info.nkx[0] = 0;
info.nky[0] = 0;
info.nkz[0] = 0;
calc_grid(stdout,state.box,info.fourier_sp[0],&(info.nkx[0]),&(info.nky[0]),&(info.nkz[0]));
if ( (ir->nkx != info.nkx[0]) || (ir->nky != info.nky[0]) || (ir->nkz != info.nkz[0]) )
gmx_fatal(FARGS, "Wrong fourierspacing %f nm, input file grid = %d x %d x %d, computed grid = %d x %d x %d",
fs,ir->nkx,ir->nky,ir->nkz,info.nkx[0],info.nky[0],info.nkz[0]);
}
/* Estimate (S)PME force error */
/* Determine the volume of the simulation box */
if (MASTER(cr))
{
info.volume = det(state.box);
calc_recipbox(state.box,info.recipbox);
info.natoms = mtop.natoms;
info.bTUNE = bTUNE;
}
if (PAR(cr))
bcast_info(&info, cr);
/* Get an error estimate of the input tpr file and do some tuning if requested */
estimate_PME_error(&info, &state, &mtop, fp, bVerbose, seed, cr);
if (MASTER(cr))
{
/* Write out optimized tpr file if requested */
if ( opt2bSet("-so",NFILE,fnm) || bTUNE )
{
ir->ewald_rtol=info.ewald_rtol[0];
write_tpx_state(opt2fn("-so",NFILE,fnm),ir,&state,&mtop);
}
please_cite(fp,"Wang2010");
fclose(fp);
}
if (gmx_parallel_env_initialized())
{
gmx_finalize();
}
return 0;
}
int main(int argc,char *argv[])
{
static char *desc[] = {
"The [TT]pmetest[tt] program tests the scaling of the PME code. When only given",
"a [TT].tpr[tt] file it will compute PME for one frame. When given a trajectory",
"it will do so for all the frames in the trajectory. Before the PME",
"routine is called the coordinates are sorted along the X-axis.[PAR]",
"As an extra service to the public the program can also compute",
"long-range Coulomb energies for components of the system. When the",
"[TT]-groups[tt] flag is given to the program the energy groups",
"from the [TT].tpr[tt] file will be read, and half an energy matrix computed."
};
t_commrec *cr,*mcr;
static t_filenm fnm[] = {
{ efTPX, NULL, NULL, ffREAD },
{ efTRN, "-o", NULL, ffWRITE },
{ efLOG, "-g", "pme", ffWRITE },
{ efTRX, "-f", NULL, ffOPTRD },
{ efXVG, "-x", "ener-pme", ffWRITE }
};
#define NFILE asize(fnm)
/* Command line options ! */
static gmx_bool bVerbose=FALSE;
static gmx_bool bOptFFT=FALSE;
static gmx_bool bSort=FALSE;
static int ewald_geometry=eewg3D;
static int nnodes=1;
static int pme_order=0;
static rvec grid = { -1, -1, -1 };
static real rc = 0.0;
static real dtol = 0.0;
static gmx_bool bGroups = FALSE;
static t_pargs pa[] = {
{ "-np", FALSE, etINT, {&nnodes},
"Number of nodes, must be the same as used for [TT]grompp[tt]" },
{ "-v", FALSE, etBOOL,{&bVerbose},
"Be loud and noisy" },
{ "-sort", FALSE, etBOOL,{&bSort},
"Sort coordinates. Crucial for domain decomposition." },
{ "-grid", FALSE, etRVEC,{&grid},
"Number of grid cells in X, Y, Z dimension (if -1 use from [TT].tpr[tt])" },
{ "-order", FALSE, etINT, {&pme_order},
"Order of the PME spreading algorithm" },
{ "-groups", FALSE, etBOOL, {&bGroups},
"Compute half an energy matrix based on the energy groups in your [TT].tpr[tt] file" },
{ "-rc", FALSE, etREAL, {&rc},
"Rcoulomb for Ewald summation" },
{ "-tol", FALSE, etREAL, {&dtol},
"Tolerance for Ewald summation" }
};
FILE *fp;
t_inputrec *ir;
t_topology top;
t_tpxheader tpx;
t_nrnb nrnb;
t_nsborder *nsb;
t_forcerec *fr;
t_mdatoms *mdatoms;
char title[STRLEN];
int natoms,step,status,i,ncg,root;
real t,lambda,ewaldcoeff,qtot;
rvec *x,*f,*xbuf;
int *index;
gmx_bool bCont;
real *charge,*qbuf,*qqbuf;
matrix box;
/* Start the actual parallel code if necessary */
cr = init_par(&argc,&argv);
root = 0;
if (MASTER(cr))
CopyRight(stderr,argv[0]);
/* Parse command line on all processors, arguments are passed on in
* init_par (see above)
*/
parse_common_args(&argc,argv,
PCA_KEEP_ARGS | PCA_NOEXIT_ON_ARGS | PCA_BE_NICE |
PCA_CAN_SET_DEFFNM | (MASTER(cr) ? 0 : PCA_QUIET),
NFILE,fnm,asize(pa),pa,asize(desc),desc,0,NULL);
#ifndef GMX_MPI
if (nnodes > 1)
gmx_fatal(FARGS,"GROMACS compiled without MPI support - can't do parallel runs");
#endif
/* Open log files on all processors */
open_log(ftp2fn(efLOG,NFILE,fnm),cr);
snew(ir,1);
if (MASTER(cr)) {
/* Read tpr file etc. */
read_tpxheader(ftp2fn(efTPX,NFILE,fnm),&tpx,FALSE,NULL,NULL);
snew(x,tpx.natoms);
read_tpx(ftp2fn(efTPX,NFILE,fnm),&step,&t,&lambda,ir,
box,&natoms,x,NULL,NULL,&top);
/* Charges */
qtot = 0;
snew(charge,natoms);
for(i=0; (i<natoms); i++) {
charge[i] = top.atoms.atom[i].q;
qtot += charge[i];
}
/* Grid stuff */
if (opt2parg_bSet("-grid",asize(pa),pa)) {
ir->nkx = grid[XX];
ir->nky = grid[YY];
ir->nkz = grid[ZZ];
}
/* Check command line parameters for consistency */
if ((ir->nkx <= 0) || (ir->nky <= 0) || (ir->nkz <= 0))
gmx_fatal(FARGS,"PME grid = %d %d %d",ir->nkx,ir->nky,ir->nkz);
if (opt2parg_bSet("-rc",asize(pa),pa))
ir->rcoulomb = rc;
if (ir->rcoulomb <= 0)
gmx_fatal(FARGS,"rcoulomb should be > 0 (not %f)",ir->rcoulomb);
if (opt2parg_bSet("-order",asize(pa),pa))
ir->pme_order = pme_order;
if (ir->pme_order <= 0)
gmx_fatal(FARGS,"pme_order should be > 0 (not %d)",ir->pme_order);
if (opt2parg_bSet("-tol",asize(pa),pa))
ir->ewald_rtol = dtol;
if (ir->ewald_rtol <= 0)
gmx_fatal(FARGS,"ewald_tol should be > 0 (not %f)",ir->ewald_rtol);
}
else {
init_top(&top);
}
/* Add parallellization code here */
snew(nsb,1);
if (MASTER(cr)) {
ncg = top.blocks[ebCGS].multinr[0];
for(i=0; (i<cr->nnodes-1); i++)
top.blocks[ebCGS].multinr[i] = min(ncg,(ncg*(i+1))/cr->nnodes);
for( ; (i<MAXNODES); i++)
top.blocks[ebCGS].multinr[i] = ncg;
}
if (PAR(cr)) {
/* Set some variables to zero to avoid core dumps */
ir->opts.ngtc = ir->opts.ngacc = ir->opts.ngfrz = ir->opts.ngener = 0;
#ifdef GMX_MPI
/* Distribute the data over processors */
MPI_Bcast(&natoms,1,MPI_INT,root,MPI_COMM_WORLD);
MPI_Bcast(ir,sizeof(*ir),MPI_BYTE,root,MPI_COMM_WORLD);
MPI_Bcast(&qtot,1,GMX_MPI_REAL,root,MPI_COMM_WORLD);
#endif
/* Call some dedicated communication routines, master sends n-1 times */
if (MASTER(cr)) {
for(i=1; (i<cr->nnodes); i++) {
mv_block(i,&(top.blocks[ebCGS]));
mv_block(i,&(top.atoms.excl));
}
}
else {
ld_block(root,&(top.blocks[ebCGS]));
ld_block(root,&(top.atoms.excl));
}
if (!MASTER(cr)) {
snew(charge,natoms);
snew(x,natoms);
}
#ifdef GMX_MPI
MPI_Bcast(charge,natoms,GMX_MPI_REAL,root,MPI_COMM_WORLD);
#endif
}
ewaldcoeff = calc_ewaldcoeff(ir->rcoulomb,ir->ewald_rtol);
if (bVerbose)
pr_inputrec(stdlog,0,"Inputrec",ir);
/* Allocate memory for temp arrays etc. */
snew(xbuf,natoms);
snew(f,natoms);
snew(qbuf,natoms);
snew(qqbuf,natoms);
snew(index,natoms);
/* Initialize the PME code */
init_pme(stdlog,cr,ir->nkx,ir->nky,ir->nkz,ir->pme_order,
natoms,FALSE,bOptFFT,ewald_geometry);
/* MFlops accounting */
init_nrnb(&nrnb);
/* Initialize the work division */
calc_nsb(stdlog,&(top.blocks[ebCGS]),cr->nnodes,nsb,0);
nsb->nodeid = cr->nodeid;
print_nsb(stdlog,"pmetest",nsb);
/* Initiate forcerec */
mdatoms = atoms2md(stdlog,&top.atoms,ir->opts.nFreeze,ir->eI,
ir->delta_t,0,ir->opts.tau_t,FALSE,FALSE);
snew(fr,1);
init_forcerec(stdlog,fr,ir,&top,cr,mdatoms,nsb,box,FALSE,NULL,NULL,FALSE);
/* First do PME based on coordinates in tpr file, send them to
* other processors if needed.
*/
if (MASTER(cr))
fprintf(stdlog,"-----\n"
"Results based on tpr file %s\n",ftp2fn(efTPX,NFILE,fnm));
#ifdef GMX_MPI
if (PAR(cr)) {
MPI_Bcast(x[0],natoms*DIM,GMX_MPI_REAL,root,MPI_COMM_WORLD);
MPI_Bcast(box[0],DIM*DIM,GMX_MPI_REAL,root,MPI_COMM_WORLD);
MPI_Bcast(&t,1,GMX_MPI_REAL,root,MPI_COMM_WORLD);
}
#endif
do_my_pme(stdlog,0,bVerbose,ir,x,xbuf,f,charge,qbuf,qqbuf,box,bSort,
cr,nsb,&nrnb,&(top.atoms.excl),qtot,fr,index,NULL,
bGroups ? ir->opts.ngener : 1,mdatoms->cENER);
/* If we have a trajectry file, we will read the frames in it and compute
* the PME energy.
*/
if (ftp2bSet(efTRX,NFILE,fnm)) {
fprintf(stdlog,"-----\n"
"Results based on trx file %s\n",ftp2fn(efTRX,NFILE,fnm));
if (MASTER(cr)) {
sfree(x);
natoms = read_first_x(&status,ftp2fn(efTRX,NFILE,fnm),&t,&x,box);
if (natoms != top.atoms.nr)
gmx_fatal(FARGS,"natoms in trx = %d, in tpr = %d",natoms,top.atoms.nr);
fp = xvgropen(ftp2fn(efXVG,NFILE,fnm),"PME Energy","Time (ps)","E (kJ/mol)");
}
else
fp = NULL;
do {
/* Send coordinates, box and time to the other nodes */
#ifdef GMX_MPI
if (PAR(cr)) {
MPI_Bcast(x[0],natoms*DIM,GMX_MPI_REAL,root,MPI_COMM_WORLD);
MPI_Bcast(box[0],DIM*DIM,GMX_MPI_REAL,root,MPI_COMM_WORLD);
MPI_Bcast(&t,1,GMX_MPI_REAL,root,MPI_COMM_WORLD);
}
#endif
rm_pbc(&top.idef,nsb->natoms,box,x,x);
/* Call the PME wrapper function */
do_my_pme(stdlog,t,bVerbose,ir,x,xbuf,f,charge,qbuf,qqbuf,box,bSort,cr,
nsb,&nrnb,&(top.atoms.excl),qtot,fr,index,fp,
bGroups ? ir->opts.ngener : 1,mdatoms->cENER);
/* Only the master processor reads more data */
if (MASTER(cr))
bCont = read_next_x(status,&t,natoms,x,box);
/* Check whether we need to continue */
#ifdef GMX_MPI
if (PAR(cr))
MPI_Bcast(&bCont,1,MPI_INT,root,MPI_COMM_WORLD);
#endif
} while (bCont);
/* Finish I/O, close files */
if (MASTER(cr)) {
close_trx(status);
ffclose(fp);
}
}
if (bVerbose) {
/* Do some final I/O about performance, might be useful in debugging */
fprintf(stdlog,"-----\n");
print_nrnb(stdlog,&nrnb);
}
/* Finish the parallel stuff */
if (gmx_parallel_env_initialized())
gmx_finalize(cr);
/* Thank the audience, as usual */
if (MASTER(cr))
thanx(stderr);
return 0;
}
int main(int argc,char *argv[])
{
int mmm[] = { 8, 10, 12, 15, 16, 18, 20, 24, 25, 27, 30, 32, 36, 40,
45, 48, 50, 54, 60, 64, 72, 75, 80, 81, 90, 100 };
int nnn[] = { 24, 32, 48, 60, 72, 84, 96 };
#define NNN asize(nnn)
FILE *fp,*fplog;
int *niter;
int i,j,n,nit,ntot,n3,rsize;
double t,nflop,start;
double *rt,*ct;
t_fftgrid *g;
t_commrec *cr;
static gmx_bool bReproducible = FALSE;
static int nnode = 1;
static int nitfac = 1;
t_pargs pa[] = {
{ "-reproducible", FALSE, etBOOL, {&bReproducible},
"Request binary reproducible results" },
{ "-np", FALSE, etINT, {&nnode},
"Number of NODEs" },
{ "-itfac", FALSE, etINT, {&nitfac},
"Multiply number of iterations by this" }
};
static t_filenm fnm[] = {
{ efLOG, "-g", "fft", ffWRITE },
{ efXVG, "-o", "fft", ffWRITE }
};
#define NFILE asize(fnm)
cr = init_par(&argc,&argv);
if (MASTER(cr))
CopyRight(stdout,argv[0]);
parse_common_args(&argc,argv,
PCA_CAN_SET_DEFFNM | (MASTER(cr) ? 0 : PCA_QUIET),
NFILE,fnm,asize(pa),pa,0,NULL,0,NULL);
gmx_log_open(ftp2fn(efLOG,NFILE,fnm),cr,1,0,&fplog);
snew(niter,NNN);
snew(ct,NNN);
snew(rt,NNN);
rsize = sizeof(real);
for(i=0; (i<NNN); i++) {
n = nnn[i];
if (n < 16)
niter[i] = 50;
else if (n < 26)
niter[i] = 20;
else if (n < 51)
niter[i] = 10;
else
niter[i] = 5;
niter[i] *= nitfac;
nit = niter[i];
if (MASTER(cr))
fprintf(stderr,"\r3D FFT (%s precision) %3d^3, niter %3d ",
(rsize == 8) ? "Double" : "Single",n,nit);
g = mk_fftgrid(n,n,n,NULL,NULL,cr,bReproducible);
if (PAR(cr))
start = time(NULL);
else
start_time();
for(j=0; (j<nit); j++) {
gmxfft3D(g,GMX_FFT_REAL_TO_COMPLEX,cr);
gmxfft3D(g,GMX_FFT_COMPLEX_TO_REAL,cr);
}
if (PAR(cr))
rt[i] = time(NULL)-start;
else {
update_time();
rt[i] = node_time();
}
done_fftgrid(g);
sfree(g);
}
if (MASTER(cr)) {
fprintf(stderr,"\n");
fp=xvgropen(ftp2fn(efXVG,NFILE,fnm),
"FFT timings","n^3","t (s)");
for(i=0; (i<NNN); i++) {
n3 = 2*niter[i]*nnn[i]*nnn[i]*nnn[i];
fprintf(fp,"%10d %10g\n",nnn[i],rt[i]/(2*niter[i]));
}
gmx_fio_fclose(fp);
}
return 0;
}
int gmx_disre(int argc,char *argv[])
{
const char *desc[] = {
"g_disre computes violations of distance restraints.",
"If necessary all protons can be added to a protein molecule ",
"using the protonate program.[PAR]",
"The program always",
"computes the instantaneous violations rather than time-averaged,",
"because this analysis is done from a trajectory file afterwards",
"it does not make sense to use time averaging. However,",
"the time averaged values per restraint are given in the log file.[PAR]",
"An index file may be used to select specific restraints for",
"printing.[PAR]",
"When the optional[TT]-q[tt] flag is given a pdb file coloured by the",
"amount of average violations.[PAR]",
"When the [TT]-c[tt] option is given, an index file will be read",
"containing the frames in your trajectory corresponding to the clusters",
"(defined in another manner) that you want to analyze. For these clusters",
"the program will compute average violations using the third power",
"averaging algorithm and print them in the log file."
};
static int ntop = 0;
static int nlevels = 20;
static real max_dr = 0;
static gmx_bool bThird = TRUE;
t_pargs pa[] = {
{ "-ntop", FALSE, etINT, {&ntop},
"Number of large violations that are stored in the log file every step" },
{ "-maxdr", FALSE, etREAL, {&max_dr},
"Maximum distance violation in matrix output. If less than or equal to 0 the maximum will be determined by the data." },
{ "-nlevels", FALSE, etINT, {&nlevels},
"Number of levels in the matrix output" },
{ "-third", FALSE, etBOOL, {&bThird},
"Use inverse third power averaging or linear for matrix output" }
};
FILE *out=NULL,*aver=NULL,*numv=NULL,*maxxv=NULL,*xvg=NULL;
t_tpxheader header;
t_inputrec ir;
gmx_mtop_t mtop;
rvec *xtop;
gmx_localtop_t *top;
t_atoms *atoms=NULL;
t_forcerec *fr;
t_fcdata fcd;
t_nrnb nrnb;
t_commrec *cr;
t_graph *g;
int ntopatoms,natoms,i,j,kkk;
t_trxstatus *status;
real t;
rvec *x,*f,*xav=NULL;
matrix box;
gmx_bool bPDB;
int isize;
atom_id *index=NULL,*ind_fit=NULL;
char *grpname;
t_cluster_ndx *clust=NULL;
t_dr_result dr,*dr_clust=NULL;
char **leg;
real *vvindex=NULL,*w_rls=NULL;
t_mdatoms *mdatoms;
t_pbc pbc,*pbc_null;
int my_clust;
FILE *fplog;
output_env_t oenv;
gmx_rmpbc_t gpbc=NULL;
t_filenm fnm[] = {
{ efTPX, NULL, NULL, ffREAD },
{ efTRX, "-f", NULL, ffREAD },
{ efXVG, "-ds", "drsum", ffWRITE },
{ efXVG, "-da", "draver", ffWRITE },
{ efXVG, "-dn", "drnum", ffWRITE },
{ efXVG, "-dm", "drmax", ffWRITE },
{ efXVG, "-dr", "restr", ffWRITE },
{ efLOG, "-l", "disres", ffWRITE },
{ efNDX, NULL, "viol", ffOPTRD },
{ efPDB, "-q", "viol", ffOPTWR },
{ efNDX, "-c", "clust", ffOPTRD },
{ efXPM, "-x", "matrix", ffOPTWR }
};
#define NFILE asize(fnm)
cr = init_par(&argc,&argv);
CopyRight(stderr,argv[0]);
parse_common_args(&argc,argv,PCA_CAN_TIME | PCA_CAN_VIEW | PCA_BE_NICE,
NFILE,fnm,asize(pa),pa,asize(desc),desc,0,NULL,&oenv);
gmx_log_open(ftp2fn(efLOG,NFILE,fnm),cr,FALSE,0,&fplog);
if (ntop)
init5(ntop);
read_tpxheader(ftp2fn(efTPX,NFILE,fnm),&header,FALSE,NULL,NULL);
snew(xtop,header.natoms);
read_tpx(ftp2fn(efTPX,NFILE,fnm),&ir,box,&ntopatoms,xtop,NULL,NULL,&mtop);
bPDB = opt2bSet("-q",NFILE,fnm);
if (bPDB) {
snew(xav,ntopatoms);
snew(ind_fit,ntopatoms);
snew(w_rls,ntopatoms);
for(kkk=0; (kkk<ntopatoms); kkk++) {
w_rls[kkk] = 1;
ind_fit[kkk] = kkk;
}
snew(atoms,1);
*atoms = gmx_mtop_global_atoms(&mtop);
if (atoms->pdbinfo == NULL) {
snew(atoms->pdbinfo,atoms->nr);
}
}
top = gmx_mtop_generate_local_top(&mtop,&ir);
g = NULL;
pbc_null = NULL;
if (ir.ePBC != epbcNONE) {
if (ir.bPeriodicMols)
pbc_null = &pbc;
else
g = mk_graph(fplog,&top->idef,0,mtop.natoms,FALSE,FALSE);
}
if (ftp2bSet(efNDX,NFILE,fnm)) {
rd_index(ftp2fn(efNDX,NFILE,fnm),1,&isize,&index,&grpname);
xvg=xvgropen(opt2fn("-dr",NFILE,fnm),"Inidividual Restraints","Time (ps)",
"nm",oenv);
snew(vvindex,isize);
snew(leg,isize);
for(i=0; (i<isize); i++) {
index[i]++;
snew(leg[i],12);
sprintf(leg[i],"index %d",index[i]);
}
xvgr_legend(xvg,isize,(const char**)leg,oenv);
}
else
isize=0;
ir.dr_tau=0.0;
init_disres(fplog,&mtop,&ir,NULL,FALSE,&fcd,NULL);
natoms=read_first_x(oenv,&status,ftp2fn(efTRX,NFILE,fnm),&t,&x,box);
snew(f,5*natoms);
init_dr_res(&dr,fcd.disres.nres);
if (opt2bSet("-c",NFILE,fnm)) {
clust = cluster_index(fplog,opt2fn("-c",NFILE,fnm));
snew(dr_clust,clust->clust->nr+1);
for(i=0; (i<=clust->clust->nr); i++)
init_dr_res(&dr_clust[i],fcd.disres.nres);
}
else {
out =xvgropen(opt2fn("-ds",NFILE,fnm),
"Sum of Violations","Time (ps)","nm",oenv);
aver=xvgropen(opt2fn("-da",NFILE,fnm),
"Average Violation","Time (ps)","nm",oenv);
numv=xvgropen(opt2fn("-dn",NFILE,fnm),
"# Violations","Time (ps)","#",oenv);
maxxv=xvgropen(opt2fn("-dm",NFILE,fnm),
"Largest Violation","Time (ps)","nm",oenv);
}
mdatoms = init_mdatoms(fplog,&mtop,ir.efep!=efepNO);
atoms2md(&mtop,&ir,0,NULL,0,mtop.natoms,mdatoms);
update_mdatoms(mdatoms,ir.init_lambda);
fr = mk_forcerec();
fprintf(fplog,"Made forcerec\n");
init_forcerec(fplog,oenv,fr,NULL,&ir,&mtop,cr,box,FALSE,NULL,NULL,NULL,
FALSE,-1);
init_nrnb(&nrnb);
if (ir.ePBC != epbcNONE)
gpbc = gmx_rmpbc_init(&top->idef,ir.ePBC,natoms,box);
j=0;
do {
if (ir.ePBC != epbcNONE) {
if (ir.bPeriodicMols)
set_pbc(&pbc,ir.ePBC,box);
else
gmx_rmpbc(gpbc,natoms,box,x);
}
if (clust) {
if (j > clust->maxframe)
gmx_fatal(FARGS,"There are more frames in the trajectory than in the cluster index file. t = %8f\n",t);
my_clust = clust->inv_clust[j];
range_check(my_clust,0,clust->clust->nr);
check_viol(fplog,cr,&(top->idef.il[F_DISRES]),
top->idef.iparams,top->idef.functype,
x,f,fr,pbc_null,g,dr_clust,my_clust,isize,index,vvindex,&fcd);
}
else
check_viol(fplog,cr,&(top->idef.il[F_DISRES]),
top->idef.iparams,top->idef.functype,
x,f,fr,pbc_null,g,&dr,0,isize,index,vvindex,&fcd);
if (bPDB) {
reset_x(atoms->nr,ind_fit,atoms->nr,NULL,x,w_rls);
do_fit(atoms->nr,w_rls,x,x);
if (j == 0) {
/* Store the first frame of the trajectory as 'characteristic'
* for colouring with violations.
*/
for(kkk=0; (kkk<atoms->nr); kkk++)
copy_rvec(x[kkk],xav[kkk]);
}
}
if (!clust) {
if (isize > 0) {
fprintf(xvg,"%10g",t);
for(i=0; (i<isize); i++)
fprintf(xvg," %10g",vvindex[i]);
fprintf(xvg,"\n");
}
fprintf(out, "%10g %10g\n",t,dr.sumv);
fprintf(aver, "%10g %10g\n",t,dr.averv);
fprintf(maxxv,"%10g %10g\n",t,dr.maxv);
fprintf(numv, "%10g %10d\n",t,dr.nv);
}
j++;
} while (read_next_x(oenv,status,&t,natoms,x,box));
close_trj(status);
if (ir.ePBC != epbcNONE)
gmx_rmpbc_done(gpbc);
if (clust) {
dump_clust_stats(fplog,fcd.disres.nres,&(top->idef.il[F_DISRES]),
top->idef.iparams,clust->clust,dr_clust,
clust->grpname,isize,index);
}
else {
dump_stats(fplog,j,fcd.disres.nres,&(top->idef.il[F_DISRES]),
top->idef.iparams,&dr,isize,index,
bPDB ? atoms : NULL);
if (bPDB) {
write_sto_conf(opt2fn("-q",NFILE,fnm),
"Coloured by average violation in Angstrom",
atoms,xav,NULL,ir.ePBC,box);
}
dump_disre_matrix(opt2fn_null("-x",NFILE,fnm),&dr,fcd.disres.nres,
j,&top->idef,&mtop,max_dr,nlevels,bThird);
ffclose(out);
ffclose(aver);
ffclose(numv);
ffclose(maxxv);
if (isize > 0) {
ffclose(xvg);
do_view(oenv,opt2fn("-dr",NFILE,fnm),"-nxy");
}
do_view(oenv,opt2fn("-dn",NFILE,fnm),"-nxy");
do_view(oenv,opt2fn("-da",NFILE,fnm),"-nxy");
do_view(oenv,opt2fn("-ds",NFILE,fnm),"-nxy");
do_view(oenv,opt2fn("-dm",NFILE,fnm),"-nxy");
}
thanx(stderr);
if (gmx_parallel_env_initialized())
gmx_finalize();
gmx_log_close(fplog);
return 0;
}
int cmain(int argc, char *argv[])
{
const char *desc[] = {
"The [TT]mdrun[tt] program is the main computational chemistry engine",
"within GROMACS. Obviously, it performs Molecular Dynamics simulations,",
"but it can also perform Stochastic Dynamics, Energy Minimization,",
"test particle insertion or (re)calculation of energies.",
"Normal mode analysis is another option. In this case [TT]mdrun[tt]",
"builds a Hessian matrix from single conformation.",
"For usual Normal Modes-like calculations, make sure that",
"the structure provided is properly energy-minimized.",
"The generated matrix can be diagonalized by [TT]g_nmeig[tt].[PAR]",
"The [TT]mdrun[tt] program reads the run input file ([TT]-s[tt])",
"and distributes the topology over nodes if needed.",
"[TT]mdrun[tt] produces at least four output files.",
"A single log file ([TT]-g[tt]) is written, unless the option",
"[TT]-seppot[tt] is used, in which case each node writes a log file.",
"The trajectory file ([TT]-o[tt]), contains coordinates, velocities and",
"optionally forces.",
"The structure file ([TT]-c[tt]) contains the coordinates and",
"velocities of the last step.",
"The energy file ([TT]-e[tt]) contains energies, the temperature,",
"pressure, etc, a lot of these things are also printed in the log file.",
"Optionally coordinates can be written to a compressed trajectory file",
"([TT]-x[tt]).[PAR]",
"The option [TT]-dhdl[tt] is only used when free energy calculation is",
"turned on.[PAR]",
"A simulation can be run in parallel using two different parallelization",
"schemes: MPI parallelization and/or OpenMP thread parallelization.",
"The MPI parallelization uses multiple processes when [TT]mdrun[tt] is",
"compiled with a normal MPI library or threads when [TT]mdrun[tt] is",
"compiled with the GROMACS built-in thread-MPI library. OpenMP threads",
"are supported when mdrun is compiled with OpenMP. Full OpenMP support",
"is only available with the Verlet cut-off scheme, with the (older)",
"group scheme only PME-only processes can use OpenMP parallelization.",
"In all cases [TT]mdrun[tt] will by default try to use all the available",
"hardware resources. With a normal MPI library only the options",
"[TT]-ntomp[tt] (with the Verlet cut-off scheme) and [TT]-ntomp_pme[tt],",
"for PME-only processes, can be used to control the number of threads.",
"With thread-MPI there are additional options [TT]-nt[tt], which sets",
"the total number of threads, and [TT]-ntmpi[tt], which sets the number",
"of thread-MPI threads.",
"Note that using combined MPI+OpenMP parallelization is almost always",
"slower than single parallelization, except at the scaling limit, where",
"especially OpenMP parallelization of PME reduces the communication cost.",
"OpenMP-only parallelization is much faster than MPI-only parallelization",
"on a single CPU(-die). Since we currently don't have proper hardware",
"topology detection, [TT]mdrun[tt] compiled with thread-MPI will only",
"automatically use OpenMP-only parallelization when you use up to 4",
"threads, up to 12 threads with Intel Nehalem/Westmere, or up to 16",
"threads with Intel Sandy Bridge or newer CPUs. Otherwise MPI-only",
"parallelization is used (except with GPUs, see below).",
"[PAR]",
"To quickly test the performance of the new Verlet cut-off scheme",
"with old [TT].tpr[tt] files, either on CPUs or CPUs+GPUs, you can use",
"the [TT]-testverlet[tt] option. This should not be used for production,",
"since it can slightly modify potentials and it will remove charge groups",
"making analysis difficult, as the [TT].tpr[tt] file will still contain",
"charge groups. For production simulations it is highly recommended",
"to specify [TT]cutoff-scheme = Verlet[tt] in the [TT].mdp[tt] file.",
"[PAR]",
"With GPUs (only supported with the Verlet cut-off scheme), the number",
"of GPUs should match the number of MPI processes or MPI threads,",
"excluding PME-only processes/threads. With thread-MPI the number",
"of MPI threads will automatically be set to the number of GPUs detected.",
"When you want to use a subset of the available GPUs, you can use",
"the [TT]-gpu_id[tt] option, where GPU id's are passed as a string,",
"e.g. 02 for using GPUs 0 and 2. When you want different GPU id's",
"on different nodes of a compute cluster, use the GMX_GPU_ID environment",
"variable instead. The format for GMX_GPU_ID is identical to ",
"[TT]-gpu_id[tt], but an environment variable can have different values",
"on different nodes of a cluster.",
"[PAR]",
"When using PME with separate PME nodes or with a GPU, the two major",
"compute tasks, the non-bonded force calculation and the PME calculation",
"run on different compute resources. If this load is not balanced,",
"some of the resources will be idle part of time. With the Verlet",
"cut-off scheme this load is automatically balanced when the PME load",
"is too high (but not when it is too low). This is done by scaling",
"the Coulomb cut-off and PME grid spacing by the same amount. In the first",
"few hundred steps different settings are tried and the fastest is chosen",
"for the rest of the simulation. This does not affect the accuracy of",
"the results, but it does affect the decomposition of the Coulomb energy",
"into particle and mesh contributions. The auto-tuning can be turned off",
"with the option [TT]-notunepme[tt].",
"[PAR]",
"[TT]mdrun[tt] pins (sets affinity of) threads to specific cores,",
"when all (logical) cores on a compute node are used by [TT]mdrun[tt],",
"even when no multi-threading is used,",
"as this usually results in significantly better performance.",
"If the queuing systems or the OpenMP library pinned threads, we honor",
"this and don't pin again, even though the layout may be sub-optimal.",
"If you want to have [TT]mdrun[tt] override an already set thread affinity",
"or pin threads when using less cores, use [TT]-pin on[tt].",
"With SMT (simultaneous multithreading), e.g. Intel Hyper-Threading,",
"there are multiple logical cores per physical core.",
"The option [TT]-pinstride[tt] sets the stride in logical cores for",
"pinning consecutive threads. Without SMT, 1 is usually the best choice.",
"With Intel Hyper-Threading 2 is best when using half or less of the",
"logical cores, 1 otherwise. The default value of 0 do exactly that:",
"it minimizes the threads per logical core, to optimize performance.",
"If you want to run multiple mdrun jobs on the same physical node,"
"you should set [TT]-pinstride[tt] to 1 when using all logical cores.",
"When running multiple mdrun (or other) simulations on the same physical",
"node, some simulations need to start pinning from a non-zero core",
"to avoid overloading cores; with [TT]-pinoffset[tt] you can specify",
"the offset in logical cores for pinning.",
"[PAR]",
"When [TT]mdrun[tt] is started using MPI with more than 1 process",
"or with thread-MPI with more than 1 thread, MPI parallelization is used.",
"By default domain decomposition is used, unless the [TT]-pd[tt]",
"option is set, which selects particle decomposition.",
"[PAR]",
"With domain decomposition, the spatial decomposition can be set",
"with option [TT]-dd[tt]. By default [TT]mdrun[tt] selects a good decomposition.",
"The user only needs to change this when the system is very inhomogeneous.",
"Dynamic load balancing is set with the option [TT]-dlb[tt],",
"which can give a significant performance improvement,",
"especially for inhomogeneous systems. The only disadvantage of",
"dynamic load balancing is that runs are no longer binary reproducible,",
"but in most cases this is not important.",
"By default the dynamic load balancing is automatically turned on",
"when the measured performance loss due to load imbalance is 5% or more.",
"At low parallelization these are the only important options",
"for domain decomposition.",
"At high parallelization the options in the next two sections",
"could be important for increasing the performace.",
"[PAR]",
"When PME is used with domain decomposition, separate nodes can",
"be assigned to do only the PME mesh calculation;",
"this is computationally more efficient starting at about 12 nodes.",
"The number of PME nodes is set with option [TT]-npme[tt],",
"this can not be more than half of the nodes.",
"By default [TT]mdrun[tt] makes a guess for the number of PME",
"nodes when the number of nodes is larger than 11 or performance wise",
"not compatible with the PME grid x dimension.",
"But the user should optimize npme. Performance statistics on this issue",
"are written at the end of the log file.",
"For good load balancing at high parallelization, the PME grid x and y",
"dimensions should be divisible by the number of PME nodes",
"(the simulation will run correctly also when this is not the case).",
"[PAR]",
"This section lists all options that affect the domain decomposition.",
"[PAR]",
"Option [TT]-rdd[tt] can be used to set the required maximum distance",
"for inter charge-group bonded interactions.",
"Communication for two-body bonded interactions below the non-bonded",
"cut-off distance always comes for free with the non-bonded communication.",
"Atoms beyond the non-bonded cut-off are only communicated when they have",
"missing bonded interactions; this means that the extra cost is minor",
"and nearly indepedent of the value of [TT]-rdd[tt].",
"With dynamic load balancing option [TT]-rdd[tt] also sets",
"the lower limit for the domain decomposition cell sizes.",
"By default [TT]-rdd[tt] is determined by [TT]mdrun[tt] based on",
"the initial coordinates. The chosen value will be a balance",
"between interaction range and communication cost.",
"[PAR]",
"When inter charge-group bonded interactions are beyond",
"the bonded cut-off distance, [TT]mdrun[tt] terminates with an error message.",
"For pair interactions and tabulated bonds",
"that do not generate exclusions, this check can be turned off",
"with the option [TT]-noddcheck[tt].",
"[PAR]",
"When constraints are present, option [TT]-rcon[tt] influences",
"the cell size limit as well.",
"Atoms connected by NC constraints, where NC is the LINCS order plus 1,",
"should not be beyond the smallest cell size. A error message is",
"generated when this happens and the user should change the decomposition",
"or decrease the LINCS order and increase the number of LINCS iterations.",
"By default [TT]mdrun[tt] estimates the minimum cell size required for P-LINCS",
"in a conservative fashion. For high parallelization it can be useful",
"to set the distance required for P-LINCS with the option [TT]-rcon[tt].",
"[PAR]",
"The [TT]-dds[tt] option sets the minimum allowed x, y and/or z scaling",
"of the cells with dynamic load balancing. [TT]mdrun[tt] will ensure that",
"the cells can scale down by at least this factor. This option is used",
"for the automated spatial decomposition (when not using [TT]-dd[tt])",
"as well as for determining the number of grid pulses, which in turn",
"sets the minimum allowed cell size. Under certain circumstances",
"the value of [TT]-dds[tt] might need to be adjusted to account for",
"high or low spatial inhomogeneity of the system.",
"[PAR]",
"The option [TT]-gcom[tt] can be used to only do global communication",
"every n steps.",
"This can improve performance for highly parallel simulations",
"where this global communication step becomes the bottleneck.",
"For a global thermostat and/or barostat the temperature",
"and/or pressure will also only be updated every [TT]-gcom[tt] steps.",
"By default it is set to the minimum of nstcalcenergy and nstlist.[PAR]",
"With [TT]-rerun[tt] an input trajectory can be given for which ",
"forces and energies will be (re)calculated. Neighbor searching will be",
"performed for every frame, unless [TT]nstlist[tt] is zero",
"(see the [TT].mdp[tt] file).[PAR]",
"ED (essential dynamics) sampling and/or additional flooding potentials",
"are switched on by using the [TT]-ei[tt] flag followed by an [TT].edi[tt]",
"file. The [TT].edi[tt] file can be produced with the [TT]make_edi[tt] tool",
"or by using options in the essdyn menu of the WHAT IF program.",
"[TT]mdrun[tt] produces a [TT].xvg[tt] output file that",
"contains projections of positions, velocities and forces onto selected",
"eigenvectors.[PAR]",
"When user-defined potential functions have been selected in the",
"[TT].mdp[tt] file the [TT]-table[tt] option is used to pass [TT]mdrun[tt]",
"a formatted table with potential functions. The file is read from",
"either the current directory or from the [TT]GMXLIB[tt] directory.",
"A number of pre-formatted tables are presented in the [TT]GMXLIB[tt] dir,",
"for 6-8, 6-9, 6-10, 6-11, 6-12 Lennard-Jones potentials with",
"normal Coulomb.",
"When pair interactions are present, a separate table for pair interaction",
"functions is read using the [TT]-tablep[tt] option.[PAR]",
"When tabulated bonded functions are present in the topology,",
"interaction functions are read using the [TT]-tableb[tt] option.",
"For each different tabulated interaction type the table file name is",
"modified in a different way: before the file extension an underscore is",
"appended, then a 'b' for bonds, an 'a' for angles or a 'd' for dihedrals",
"and finally the table number of the interaction type.[PAR]",
"The options [TT]-px[tt] and [TT]-pf[tt] are used for writing pull COM",
"coordinates and forces when pulling is selected",
"in the [TT].mdp[tt] file.[PAR]",
"With [TT]-multi[tt] or [TT]-multidir[tt], multiple systems can be ",
"simulated in parallel.",
"As many input files/directories are required as the number of systems. ",
"The [TT]-multidir[tt] option takes a list of directories (one for each ",
"system) and runs in each of them, using the input/output file names, ",
"such as specified by e.g. the [TT]-s[tt] option, relative to these ",
"directories.",
"With [TT]-multi[tt], the system number is appended to the run input ",
"and each output filename, for instance [TT]topol.tpr[tt] becomes",
"[TT]topol0.tpr[tt], [TT]topol1.tpr[tt] etc.",
"The number of nodes per system is the total number of nodes",
"divided by the number of systems.",
"One use of this option is for NMR refinement: when distance",
"or orientation restraints are present these can be ensemble averaged",
"over all the systems.[PAR]",
"With [TT]-replex[tt] replica exchange is attempted every given number",
"of steps. The number of replicas is set with the [TT]-multi[tt] or ",
"[TT]-multidir[tt] option, described above.",
"All run input files should use a different coupling temperature,",
"the order of the files is not important. The random seed is set with",
"[TT]-reseed[tt]. The velocities are scaled and neighbor searching",
"is performed after every exchange.[PAR]",
"Finally some experimental algorithms can be tested when the",
"appropriate options have been given. Currently under",
"investigation are: polarizability and X-ray bombardments.",
"[PAR]",
"The option [TT]-membed[tt] does what used to be g_membed, i.e. embed",
"a protein into a membrane. The data file should contain the options",
"that where passed to g_membed before. The [TT]-mn[tt] and [TT]-mp[tt]",
"both apply to this as well.",
"[PAR]",
"The option [TT]-pforce[tt] is useful when you suspect a simulation",
"crashes due to too large forces. With this option coordinates and",
"forces of atoms with a force larger than a certain value will",
"be printed to stderr.",
"[PAR]",
"Checkpoints containing the complete state of the system are written",
"at regular intervals (option [TT]-cpt[tt]) to the file [TT]-cpo[tt],",
"unless option [TT]-cpt[tt] is set to -1.",
"The previous checkpoint is backed up to [TT]state_prev.cpt[tt] to",
"make sure that a recent state of the system is always available,",
"even when the simulation is terminated while writing a checkpoint.",
"With [TT]-cpnum[tt] all checkpoint files are kept and appended",
"with the step number.",
"A simulation can be continued by reading the full state from file",
"with option [TT]-cpi[tt]. This option is intelligent in the way that",
"if no checkpoint file is found, Gromacs just assumes a normal run and",
"starts from the first step of the [TT].tpr[tt] file. By default the output",
"will be appending to the existing output files. The checkpoint file",
"contains checksums of all output files, such that you will never",
"loose data when some output files are modified, corrupt or removed.",
"There are three scenarios with [TT]-cpi[tt]:[PAR]",
"[TT]*[tt] no files with matching names are present: new output files are written[PAR]",
"[TT]*[tt] all files are present with names and checksums matching those stored",
"in the checkpoint file: files are appended[PAR]",
"[TT]*[tt] otherwise no files are modified and a fatal error is generated[PAR]",
"With [TT]-noappend[tt] new output files are opened and the simulation",
"part number is added to all output file names.",
"Note that in all cases the checkpoint file itself is not renamed",
"and will be overwritten, unless its name does not match",
"the [TT]-cpo[tt] option.",
"[PAR]",
"With checkpointing the output is appended to previously written",
"output files, unless [TT]-noappend[tt] is used or none of the previous",
"output files are present (except for the checkpoint file).",
"The integrity of the files to be appended is verified using checksums",
"which are stored in the checkpoint file. This ensures that output can",
"not be mixed up or corrupted due to file appending. When only some",
"of the previous output files are present, a fatal error is generated",
"and no old output files are modified and no new output files are opened.",
"The result with appending will be the same as from a single run.",
"The contents will be binary identical, unless you use a different number",
"of nodes or dynamic load balancing or the FFT library uses optimizations",
"through timing.",
"[PAR]",
"With option [TT]-maxh[tt] a simulation is terminated and a checkpoint",
"file is written at the first neighbor search step where the run time",
"exceeds [TT]-maxh[tt]*0.99 hours.",
"[PAR]",
"When [TT]mdrun[tt] receives a TERM signal, it will set nsteps to the current",
"step plus one. When [TT]mdrun[tt] receives an INT signal (e.g. when ctrl+C is",
"pressed), it will stop after the next neighbor search step ",
"(with nstlist=0 at the next step).",
"In both cases all the usual output will be written to file.",
"When running with MPI, a signal to one of the [TT]mdrun[tt] processes",
"is sufficient, this signal should not be sent to mpirun or",
"the [TT]mdrun[tt] process that is the parent of the others.",
"[PAR]",
"When [TT]mdrun[tt] is started with MPI, it does not run niced by default."
};
t_commrec *cr;
t_filenm fnm[] = {
{ efTPX, NULL, NULL, ffREAD },
{ efTRN, "-o", NULL, ffWRITE },
{ efXTC, "-x", NULL, ffOPTWR },
{ efCPT, "-cpi", NULL, ffOPTRD },
{ efCPT, "-cpo", NULL, ffOPTWR },
{ efSTO, "-c", "confout", ffWRITE },
{ efEDR, "-e", "ener", ffWRITE },
{ efLOG, "-g", "md", ffWRITE },
{ efXVG, "-dhdl", "dhdl", ffOPTWR },
{ efXVG, "-field", "field", ffOPTWR },
{ efXVG, "-table", "table", ffOPTRD },
{ efXVG, "-tabletf", "tabletf", ffOPTRD },
{ efXVG, "-tablep", "tablep", ffOPTRD },
{ efXVG, "-tableb", "table", ffOPTRD },
{ efTRX, "-rerun", "rerun", ffOPTRD },
{ efXVG, "-tpi", "tpi", ffOPTWR },
{ efXVG, "-tpid", "tpidist", ffOPTWR },
{ efEDI, "-ei", "sam", ffOPTRD },
{ efXVG, "-eo", "edsam", ffOPTWR },
{ efGCT, "-j", "wham", ffOPTRD },
{ efGCT, "-jo", "bam", ffOPTWR },
{ efXVG, "-ffout", "gct", ffOPTWR },
{ efXVG, "-devout", "deviatie", ffOPTWR },
{ efXVG, "-runav", "runaver", ffOPTWR },
{ efXVG, "-px", "pullx", ffOPTWR },
{ efXVG, "-pf", "pullf", ffOPTWR },
{ efXVG, "-ro", "rotation", ffOPTWR },
{ efLOG, "-ra", "rotangles", ffOPTWR },
{ efLOG, "-rs", "rotslabs", ffOPTWR },
{ efLOG, "-rt", "rottorque", ffOPTWR },
{ efMTX, "-mtx", "nm", ffOPTWR },
{ efNDX, "-dn", "dipole", ffOPTWR },
{ efRND, "-multidir", NULL, ffOPTRDMULT},
{ efDAT, "-plumed", "plumed", ffOPTRD }, /* PLUMED */
{ efDAT, "-membed", "membed", ffOPTRD },
{ efTOP, "-mp", "membed", ffOPTRD },
{ efNDX, "-mn", "membed", ffOPTRD }
};
#define NFILE asize(fnm)
/* Command line options ! */
gmx_bool bCart = FALSE;
gmx_bool bPPPME = FALSE;
gmx_bool bPartDec = FALSE;
gmx_bool bDDBondCheck = TRUE;
gmx_bool bDDBondComm = TRUE;
gmx_bool bTunePME = TRUE;
gmx_bool bTestVerlet = FALSE;
gmx_bool bVerbose = FALSE;
gmx_bool bCompact = TRUE;
gmx_bool bSepPot = FALSE;
gmx_bool bRerunVSite = FALSE;
gmx_bool bIonize = FALSE;
gmx_bool bConfout = TRUE;
gmx_bool bReproducible = FALSE;
int npme = -1;
int nmultisim = 0;
int nstglobalcomm = -1;
int repl_ex_nst = 0;
int repl_ex_seed = -1;
int repl_ex_nex = 0;
int nstepout = 100;
int resetstep = -1;
gmx_large_int_t nsteps = -2; /* the value -2 means that the mdp option will be used */
rvec realddxyz = {0, 0, 0};
const char *ddno_opt[ddnoNR+1] =
{ NULL, "interleave", "pp_pme", "cartesian", NULL };
const char *dddlb_opt[] =
{ NULL, "auto", "no", "yes", NULL };
const char *thread_aff_opt[threadaffNR+1] =
{ NULL, "auto", "on", "off", NULL };
const char *nbpu_opt[] =
{ NULL, "auto", "cpu", "gpu", "gpu_cpu", NULL };
real rdd = 0.0, rconstr = 0.0, dlb_scale = 0.8, pforce = -1;
char *ddcsx = NULL, *ddcsy = NULL, *ddcsz = NULL;
real cpt_period = 15.0, max_hours = -1;
gmx_bool bAppendFiles = TRUE;
gmx_bool bKeepAndNumCPT = FALSE;
gmx_bool bResetCountersHalfWay = FALSE;
output_env_t oenv = NULL;
const char *deviceOptions = "";
gmx_hw_opt_t hw_opt = {0, 0, 0, 0, threadaffSEL, 0, 0, NULL};
t_pargs pa[] = {
{ "-pd", FALSE, etBOOL, {&bPartDec},
"Use particle decompostion" },
{ "-dd", FALSE, etRVEC, {&realddxyz},
"Domain decomposition grid, 0 is optimize" },
{ "-ddorder", FALSE, etENUM, {ddno_opt},
"DD node order" },
{ "-npme", FALSE, etINT, {&npme},
"Number of separate nodes to be used for PME, -1 is guess" },
{ "-nt", FALSE, etINT, {&hw_opt.nthreads_tot},
"Total number of threads to start (0 is guess)" },
{ "-ntmpi", FALSE, etINT, {&hw_opt.nthreads_tmpi},
"Number of thread-MPI threads to start (0 is guess)" },
{ "-ntomp", FALSE, etINT, {&hw_opt.nthreads_omp},
"Number of OpenMP threads per MPI process/thread to start (0 is guess)" },
{ "-ntomp_pme", FALSE, etINT, {&hw_opt.nthreads_omp_pme},
"Number of OpenMP threads per MPI process/thread to start (0 is -ntomp)" },
{ "-pin", FALSE, etENUM, {thread_aff_opt},
"Fix threads (or processes) to specific cores" },
{ "-pinoffset", FALSE, etINT, {&hw_opt.core_pinning_offset},
"The starting logical core number for pinning to cores; used to avoid pinning threads from different mdrun instances to the same core" },
{ "-pinstride", FALSE, etINT, {&hw_opt.core_pinning_stride},
"Pinning distance in logical cores for threads, use 0 to minimize the number of threads per physical core" },
{ "-gpu_id", FALSE, etSTR, {&hw_opt.gpu_id},
"List of GPU id's to use" },
{ "-ddcheck", FALSE, etBOOL, {&bDDBondCheck},
"Check for all bonded interactions with DD" },
{ "-ddbondcomm", FALSE, etBOOL, {&bDDBondComm},
"HIDDENUse special bonded atom communication when [TT]-rdd[tt] > cut-off" },
{ "-rdd", FALSE, etREAL, {&rdd},
"The maximum distance for bonded interactions with DD (nm), 0 is determine from initial coordinates" },
{ "-rcon", FALSE, etREAL, {&rconstr},
"Maximum distance for P-LINCS (nm), 0 is estimate" },
{ "-dlb", FALSE, etENUM, {dddlb_opt},
"Dynamic load balancing (with DD)" },
{ "-dds", FALSE, etREAL, {&dlb_scale},
"Minimum allowed dlb scaling of the DD cell size" },
{ "-ddcsx", FALSE, etSTR, {&ddcsx},
"HIDDENThe DD cell sizes in x" },
{ "-ddcsy", FALSE, etSTR, {&ddcsy},
"HIDDENThe DD cell sizes in y" },
{ "-ddcsz", FALSE, etSTR, {&ddcsz},
"HIDDENThe DD cell sizes in z" },
{ "-gcom", FALSE, etINT, {&nstglobalcomm},
"Global communication frequency" },
{ "-nb", FALSE, etENUM, {&nbpu_opt},
"Calculate non-bonded interactions on" },
{ "-tunepme", FALSE, etBOOL, {&bTunePME},
"Optimize PME load between PP/PME nodes or GPU/CPU" },
{ "-testverlet", FALSE, etBOOL, {&bTestVerlet},
"Test the Verlet non-bonded scheme" },
{ "-v", FALSE, etBOOL, {&bVerbose},
"Be loud and noisy" },
{ "-compact", FALSE, etBOOL, {&bCompact},
"Write a compact log file" },
{ "-seppot", FALSE, etBOOL, {&bSepPot},
"Write separate V and dVdl terms for each interaction type and node to the log file(s)" },
{ "-pforce", FALSE, etREAL, {&pforce},
"Print all forces larger than this (kJ/mol nm)" },
{ "-reprod", FALSE, etBOOL, {&bReproducible},
"Try to avoid optimizations that affect binary reproducibility" },
{ "-cpt", FALSE, etREAL, {&cpt_period},
"Checkpoint interval (minutes)" },
{ "-cpnum", FALSE, etBOOL, {&bKeepAndNumCPT},
"Keep and number checkpoint files" },
{ "-append", FALSE, etBOOL, {&bAppendFiles},
"Append to previous output files when continuing from checkpoint instead of adding the simulation part number to all file names" },
{ "-nsteps", FALSE, etGMX_LARGE_INT, {&nsteps},
"Run this number of steps, overrides .mdp file option" },
{ "-maxh", FALSE, etREAL, {&max_hours},
"Terminate after 0.99 times this time (hours)" },
{ "-multi", FALSE, etINT, {&nmultisim},
"Do multiple simulations in parallel" },
{ "-replex", FALSE, etINT, {&repl_ex_nst},
"Attempt replica exchange periodically with this period (steps)" },
{ "-nex", FALSE, etINT, {&repl_ex_nex},
"Number of random exchanges to carry out each exchange interval (N^3 is one suggestion). -nex zero or not specified gives neighbor replica exchange." },
{ "-reseed", FALSE, etINT, {&repl_ex_seed},
"Seed for replica exchange, -1 is generate a seed" },
{ "-rerunvsite", FALSE, etBOOL, {&bRerunVSite},
"HIDDENRecalculate virtual site coordinates with [TT]-rerun[tt]" },
{ "-ionize", FALSE, etBOOL, {&bIonize},
"Do a simulation including the effect of an X-Ray bombardment on your system" },
{ "-confout", FALSE, etBOOL, {&bConfout},
"HIDDENWrite the last configuration with [TT]-c[tt] and force checkpointing at the last step" },
{ "-stepout", FALSE, etINT, {&nstepout},
"HIDDENFrequency of writing the remaining runtime" },
{ "-resetstep", FALSE, etINT, {&resetstep},
"HIDDENReset cycle counters after these many time steps" },
{ "-resethway", FALSE, etBOOL, {&bResetCountersHalfWay},
"HIDDENReset the cycle counters after half the number of steps or halfway [TT]-maxh[tt]" }
};
gmx_edsam_t ed;
unsigned long Flags, PCA_Flags;
ivec ddxyz;
int dd_node_order;
gmx_bool bAddPart;
FILE *fplog, *fpmulti;
int sim_part, sim_part_fn;
const char *part_suffix = ".part";
char suffix[STRLEN];
int rc;
char **multidir = NULL;
cr = init_par(&argc, &argv);
if (MASTER(cr))
{
CopyRight(stderr, argv[0]);
}
PCA_Flags = (PCA_CAN_SET_DEFFNM | (MASTER(cr) ? 0 : PCA_QUIET));
/* Comment this in to do fexist calls only on master
* works not with rerun or tables at the moment
* also comment out the version of init_forcerec in md.c
* with NULL instead of opt2fn
*/
/*
if (!MASTER(cr))
{
PCA_Flags |= PCA_NOT_READ_NODE;
}
*/
parse_common_args(&argc, argv, PCA_Flags, NFILE, fnm, asize(pa), pa,
asize(desc), desc, 0, NULL, &oenv);
/* we set these early because they might be used in init_multisystem()
Note that there is the potential for npme>nnodes until the number of
threads is set later on, if there's thread parallelization. That shouldn't
lead to problems. */
dd_node_order = nenum(ddno_opt);
cr->npmenodes = npme;
hw_opt.thread_affinity = nenum(thread_aff_opt);
/* now check the -multi and -multidir option */
if (opt2bSet("-multidir", NFILE, fnm))
{
int i;
if (nmultisim > 0)
{
gmx_fatal(FARGS, "mdrun -multi and -multidir options are mutually exclusive.");
}
nmultisim = opt2fns(&multidir, "-multidir", NFILE, fnm);
}
if (repl_ex_nst != 0 && nmultisim < 2)
{
gmx_fatal(FARGS, "Need at least two replicas for replica exchange (option -multi)");
}
if (repl_ex_nex < 0)
{
gmx_fatal(FARGS, "Replica exchange number of exchanges needs to be positive");
}
if (nmultisim > 1)
{
#ifndef GMX_THREAD_MPI
gmx_bool bParFn = (multidir == NULL);
init_multisystem(cr, nmultisim, multidir, NFILE, fnm, bParFn);
#else
gmx_fatal(FARGS, "mdrun -multi is not supported with the thread library.Please compile GROMACS with MPI support");
#endif
}
bAddPart = !bAppendFiles;
/* Check if there is ANY checkpoint file available */
sim_part = 1;
sim_part_fn = sim_part;
if (opt2bSet("-cpi", NFILE, fnm))
{
if (bSepPot && bAppendFiles)
{
gmx_fatal(FARGS, "Output file appending is not supported with -seppot");
}
bAppendFiles =
read_checkpoint_simulation_part(opt2fn_master("-cpi", NFILE,
fnm, cr),
&sim_part_fn, NULL, cr,
bAppendFiles, NFILE, fnm,
part_suffix, &bAddPart);
if (sim_part_fn == 0 && MULTIMASTER(cr))
{
fprintf(stdout, "No previous checkpoint file present, assuming this is a new run.\n");
}
else
{
sim_part = sim_part_fn + 1;
}
if (MULTISIM(cr) && MASTER(cr))
{
if (MULTIMASTER(cr))
{
/* Log file is not yet available, so if there's a
* problem we can only write to stderr. */
fpmulti = stderr;
}
else
{
fpmulti = NULL;
}
check_multi_int(fpmulti, cr->ms, sim_part, "simulation part", TRUE);
}
}
else
{
bAppendFiles = FALSE;
}
if (!bAppendFiles)
{
sim_part_fn = sim_part;
}
if (bAddPart)
{
/* Rename all output files (except checkpoint files) */
/* create new part name first (zero-filled) */
sprintf(suffix, "%s%04d", part_suffix, sim_part_fn);
add_suffix_to_output_names(fnm, NFILE, suffix);
if (MULTIMASTER(cr))
{
fprintf(stdout, "Checkpoint file is from part %d, new output files will be suffixed '%s'.\n", sim_part-1, suffix);
}
}
Flags = opt2bSet("-rerun", NFILE, fnm) ? MD_RERUN : 0;
Flags = Flags | (bSepPot ? MD_SEPPOT : 0);
Flags = Flags | (bIonize ? MD_IONIZE : 0);
Flags = Flags | (bPartDec ? MD_PARTDEC : 0);
Flags = Flags | (bDDBondCheck ? MD_DDBONDCHECK : 0);
Flags = Flags | (bDDBondComm ? MD_DDBONDCOMM : 0);
Flags = Flags | (bTunePME ? MD_TUNEPME : 0);
Flags = Flags | (bTestVerlet ? MD_TESTVERLET : 0);
Flags = Flags | (bConfout ? MD_CONFOUT : 0);
Flags = Flags | (bRerunVSite ? MD_RERUN_VSITE : 0);
Flags = Flags | (bReproducible ? MD_REPRODUCIBLE : 0);
Flags = Flags | (bAppendFiles ? MD_APPENDFILES : 0);
Flags = Flags | (opt2parg_bSet("-append", asize(pa), pa) ? MD_APPENDFILESSET : 0);
Flags = Flags | (bKeepAndNumCPT ? MD_KEEPANDNUMCPT : 0);
Flags = Flags | (sim_part > 1 ? MD_STARTFROMCPT : 0);
Flags = Flags | (bResetCountersHalfWay ? MD_RESETCOUNTERSHALFWAY : 0);
/* We postpone opening the log file if we are appending, so we can
first truncate the old log file and append to the correct position
there instead. */
if ((MASTER(cr) || bSepPot) && !bAppendFiles)
{
gmx_log_open(ftp2fn(efLOG, NFILE, fnm), cr,
!bSepPot, Flags & MD_APPENDFILES, &fplog);
CopyRight(fplog, argv[0]);
please_cite(fplog, "Hess2008b");
please_cite(fplog, "Spoel2005a");
please_cite(fplog, "Lindahl2001a");
please_cite(fplog, "Berendsen95a");
}
else if (!MASTER(cr) && bSepPot)
{
gmx_log_open(ftp2fn(efLOG, NFILE, fnm), cr, !bSepPot, Flags, &fplog);
}
else
{
fplog = NULL;
}
ddxyz[XX] = (int)(realddxyz[XX] + 0.5);
ddxyz[YY] = (int)(realddxyz[YY] + 0.5);
ddxyz[ZZ] = (int)(realddxyz[ZZ] + 0.5);
/* PLUMED */
plumedswitch=0;
if (opt2bSet("-plumed",NFILE,fnm)) plumedswitch=1;
if(plumedswitch){
int plumed_is_there=0;
int real_precision=sizeof(real);
real energyUnits=1.0;
real lengthUnits=1.0;
real timeUnits=1.0;
if(!plumed_installed()){
gmx_fatal(FARGS,"Plumed is not available. Check your PLUMED_KERNEL variable.");
}
plumedmain=plumed_create();
plumed_cmd(plumedmain,"setRealPrecision",&real_precision);
// this is not necessary for gromacs units:
plumed_cmd(plumedmain,"setMDEnergyUnits",&energyUnits);
plumed_cmd(plumedmain,"setMDLengthUnits",&lengthUnits);
plumed_cmd(plumedmain,"setMDTimeUnits",&timeUnits);
//
plumed_cmd(plumedmain,"setPlumedDat",ftp2fn(efDAT,NFILE,fnm));
plumedswitch=1;
}
/* END PLUMED */
rc = mdrunner(&hw_opt, fplog, cr, NFILE, fnm, oenv, bVerbose, bCompact,
nstglobalcomm, ddxyz, dd_node_order, rdd, rconstr,
dddlb_opt[0], dlb_scale, ddcsx, ddcsy, ddcsz,
nbpu_opt[0],
nsteps, nstepout, resetstep,
nmultisim, repl_ex_nst, repl_ex_nex, repl_ex_seed,
pforce, cpt_period, max_hours, deviceOptions, Flags);
/* PLUMED */
if(plumedswitch){
plumed_finalize(plumedmain);
}
/* END PLUMED */
gmx_finalize_par();
if (MULTIMASTER(cr))
{
thanx(stderr);
}
/* Log file has to be closed in mdrunner if we are appending to it
(fplog not set here) */
if (MASTER(cr) && !bAppendFiles)
{
gmx_log_close(fplog);
}
return rc;
}
int gmx_nmeig(int argc,char *argv[])
{
const char *desc[] = {
"g_nmeig calculates the eigenvectors/values of a (Hessian) matrix,",
"which can be calculated with [TT]mdrun[tt].",
"The eigenvectors are written to a trajectory file ([TT]-v[tt]).",
"The structure is written first with t=0. The eigenvectors",
"are written as frames with the eigenvector number as timestamp.",
"The eigenvectors can be analyzed with [TT]g_anaeig[tt].",
"An ensemble of structures can be generated from the eigenvectors with",
"[TT]g_nmens[tt]. When mass weighting is used, the generated eigenvectors",
"will be scaled back to plain cartesian coordinates before generating the",
"output - in this case they will no longer be exactly orthogonal in the",
"standard cartesian norm (But in the mass weighted norm they would be)."
};
static gmx_bool bM=TRUE;
static int begin=1,end=50;
t_pargs pa[] =
{
{ "-m", FALSE, etBOOL, {&bM},
"Divide elements of Hessian by product of sqrt(mass) of involved "
"atoms prior to diagonalization. This should be used for 'Normal Modes' "
"analysis" },
{ "-first", FALSE, etINT, {&begin},
"First eigenvector to write away" },
{ "-last", FALSE, etINT, {&end},
"Last eigenvector to write away" }
};
FILE *out;
int status,trjout;
t_topology top;
int ePBC;
rvec *top_x;
matrix box;
real *eigenvalues;
real *eigenvectors;
real rdum,mass_fac;
int natoms,ndim,nrow,ncol,count;
char *grpname,title[256];
int i,j,k,l,d,gnx;
gmx_bool bSuck;
atom_id *index;
real value;
real factor_gmx_to_omega2;
real factor_omega_to_wavenumber;
t_commrec *cr;
output_env_t oenv;
real * full_hessian = NULL;
gmx_sparsematrix_t * sparse_hessian = NULL;
t_filenm fnm[] = {
{ efMTX, "-f", "hessian", ffREAD },
{ efTPS, NULL, NULL, ffREAD },
{ efXVG, "-of", "eigenfreq", ffWRITE },
{ efXVG, "-ol", "eigenval", ffWRITE },
{ efTRN, "-v", "eigenvec", ffWRITE }
};
#define NFILE asize(fnm)
cr = init_par(&argc,&argv);
if(MASTER(cr))
CopyRight(stderr,argv[0]);
parse_common_args(&argc,argv,PCA_BE_NICE | (MASTER(cr) ? 0 : PCA_QUIET),
NFILE,fnm,asize(pa),pa,asize(desc),desc,0,NULL,&oenv);
read_tps_conf(ftp2fn(efTPS,NFILE,fnm),title,&top,&ePBC,&top_x,NULL,box,bM);
natoms = top.atoms.nr;
ndim = DIM*natoms;
if(begin<1)
begin = 1;
if(end>ndim)
end = ndim;
/*open Hessian matrix */
gmx_mtxio_read(ftp2fn(efMTX,NFILE,fnm),&nrow,&ncol,&full_hessian,&sparse_hessian);
/* Memory for eigenvalues and eigenvectors (begin..end) */
snew(eigenvalues,nrow);
snew(eigenvectors,nrow*(end-begin+1));
/* If the Hessian is in sparse format we can calculate max (ndim-1) eigenvectors,
* and they must start at the first one. If this is not valid we convert to full matrix
* storage, but warn the user that we might run out of memory...
*/
if((sparse_hessian != NULL) && (begin!=1 || end==ndim))
{
if(begin!=1)
{
fprintf(stderr,"Cannot use sparse Hessian with first eigenvector != 1.\n");
}
else if(end==ndim)
{
fprintf(stderr,"Cannot use sparse Hessian to calculate all eigenvectors.\n");
}
fprintf(stderr,"Will try to allocate memory and convert to full matrix representation...\n");
snew(full_hessian,nrow*ncol);
for(i=0;i<nrow*ncol;i++)
full_hessian[i] = 0;
for(i=0;i<sparse_hessian->nrow;i++)
{
for(j=0;j<sparse_hessian->ndata[i];j++)
{
k = sparse_hessian->data[i][j].col;
value = sparse_hessian->data[i][j].value;
full_hessian[i*ndim+k] = value;
full_hessian[k*ndim+i] = value;
}
}
gmx_sparsematrix_destroy(sparse_hessian);
sparse_hessian = NULL;
fprintf(stderr,"Converted sparse to full matrix storage.\n");
}
if(full_hessian != NULL)
{
/* Using full matrix storage */
nma_full_hessian(full_hessian,nrow,bM,&top,begin,end,eigenvalues,eigenvectors);
}
else
{
/* Sparse memory storage, allocate memory for eigenvectors */
snew(eigenvectors,ncol*end);
nma_sparse_hessian(sparse_hessian,bM,&top,end,eigenvalues,eigenvectors);
}
/* check the output, first 6 eigenvalues should be reasonably small */
bSuck=FALSE;
for (i=begin-1; (i<6); i++)
{
if (fabs(eigenvalues[i]) > 1.0e-3)
bSuck=TRUE;
}
if (bSuck)
{
fprintf(stderr,"\nOne of the lowest 6 eigenvalues has a non-zero value.\n");
fprintf(stderr,"This could mean that the reference structure was not\n");
fprintf(stderr,"properly energy minimized.\n");
}
/* now write the output */
fprintf (stderr,"Writing eigenvalues...\n");
out=xvgropen(opt2fn("-ol",NFILE,fnm),
"Eigenvalues","Eigenvalue index","Eigenvalue [Gromacs units]",
oenv);
if (output_env_get_print_xvgr_codes(oenv)) {
if (bM)
fprintf(out,"@ subtitle \"mass weighted\"\n");
else
fprintf(out,"@ subtitle \"not mass weighted\"\n");
}
for (i=0; i<=(end-begin); i++)
fprintf (out,"%6d %15g\n",begin+i,eigenvalues[i]);
ffclose(out);
fprintf(stderr,"Writing eigenfrequencies - negative eigenvalues will be set to zero.\n");
out=xvgropen(opt2fn("-of",NFILE,fnm),
"Eigenfrequencies","Eigenvector index","Wavenumber [cm\\S-1\\N]",
oenv);
if (output_env_get_print_xvgr_codes(oenv)) {
if (bM)
fprintf(out,"@ subtitle \"mass weighted\"\n");
else
fprintf(out,"@ subtitle \"not mass weighted\"\n");
}
/* Gromacs units are kJ/(mol*nm*nm*amu),
* where amu is the atomic mass unit.
*
* For the eigenfrequencies we want to convert this to spectroscopic absorption
* wavenumbers given in cm^(-1), which is the frequency divided by the speed of
* light. Do this by first converting to omega^2 (units 1/s), take the square
* root, and finally divide by the speed of light (nm/ps in gromacs).
*/
factor_gmx_to_omega2 = 1.0E21/(AVOGADRO*AMU);
factor_omega_to_wavenumber = 1.0E-5/(2.0*M_PI*SPEED_OF_LIGHT);
for (i=0; i<=(end-begin); i++)
{
value = eigenvalues[i];
if(value < 0)
value = 0;
value=sqrt(value*factor_gmx_to_omega2)*factor_omega_to_wavenumber;
fprintf (out,"%6d %15g\n",begin+i,value);
}
ffclose(out);
/* Writing eigenvectors. Note that if mass scaling was used, the eigenvectors
* were scaled back from mass weighted cartesian to plain cartesian in the
* nma_full_hessian() or nma_sparse_hessian() routines. Mass scaled vectors
* will not be strictly orthogonal in plain cartesian scalar products.
*/
write_eigenvectors(opt2fn("-v",NFILE,fnm),natoms,eigenvectors,FALSE,begin,end,
eWXR_NO,NULL,FALSE,top_x,bM,eigenvalues);
thanx(stderr);
return 0;
}
int gmx_pme_error(int argc,char *argv[])
{
const char *desc[] = {
"g_pme_error estimates the error of the electrostatic forces",
"if using the SPME algorithm. The flag [TT]-tune[tt] will determine",
"the splitting parameter such that the error is equally",
"distributed over the real and reciprocal space part.",
"As a part of the error stems from self interaction of the particles "
"and is computationally very demanding a good a approximation is possible",
"if just a fraction of the particles is used to calculate the average",
"of this error by using the flag [TT]-self[tt].[PAR]",
};
int repeats=2;
real fs=0.0; /* 0 indicates: not set by the user */
real user_beta=-1.0;
real fracself=-1.0;
t_perf **perfdata;
t_inputinfo info;
t_state state; /* The state from the tpr input file */
gmx_mtop_t mtop; /* The topology from the tpr input file */
t_inputrec *ir=NULL; /* The inputrec from the tpr file */
FILE *fp=NULL;
t_commrec *cr;
unsigned long PCA_Flags;
gmx_bool bTUNE=FALSE;
static t_filenm fnm[] = {
/* g_tune_pme */
{ efTPX, "-s", NULL, ffREAD },
{ efOUT, "-o", "error", ffWRITE },
{ efTPX, "-so", "tuned", ffOPTWR }
};
output_env_t oenv=NULL;
t_pargs pa[] = {
/***********************/
/* g_tune_pme options: */
/***********************/
{ "-beta", FALSE, etREAL, {&user_beta},
"If positive, overwrite ewald_beta from tpr file with this value" },
{ "-tune", FALSE, etBOOL, {&bTUNE},
"If flag is set the splitting parameter will be tuned to distribute the error equally in real and rec. space" },
{ "-self", FALSE, etREAL, {&fracself},
"If positive, determine selfinteraction error just over this fraction (default=1.0)" }
};
#define NFILE asize(fnm)
cr = init_par(&argc,&argv);
if (MASTER(cr))
CopyRight(stderr,argv[0]);
PCA_Flags = PCA_NOEXIT_ON_ARGS;
PCA_Flags |= (MASTER(cr) ? 0 : PCA_QUIET);
parse_common_args(&argc,argv,PCA_Flags,
NFILE,fnm,asize(pa),pa,asize(desc),desc,
0,NULL,&oenv);
if (!bTUNE)
bTUNE = opt2bSet("-so",NFILE,fnm);
info.n_entries = 1;
/* Allocate memory for the inputinfo struct: */
create_info(&info);
info.fourier_sp[0] = fs;
/* Read in the tpr file and open logfile for reading */
if (MASTER(cr))
{
snew(ir,1);
read_tpr_file(opt2fn("-s",NFILE,fnm), &info, &state, &mtop, ir, user_beta,fracself);
fp=fopen(opt2fn("-o",NFILE,fnm),"w");
}
/* Check consistency if the user provided fourierspacing */
if (fs > 0 && MASTER(cr))
{
/* Recalculate the grid dimensions using fourierspacing from user input */
info.nkx[0] = 0;
info.nky[0] = 0;
info.nkz[0] = 0;
calc_grid(stdout,state.box,info.fourier_sp[0],&(info.nkx[0]),&(info.nky[0]),&(info.nkz[0]));
if ( (ir->nkx != info.nkx[0]) || (ir->nky != info.nky[0]) || (ir->nkz != info.nkz[0]) )
gmx_fatal(FARGS, "Wrong fourierspacing %f nm, input file grid = %d x %d x %d, computed grid = %d x %d x %d",
fs,ir->nkx,ir->nky,ir->nkz,info.nkx[0],info.nky[0],info.nkz[0]);
}
/* Estimate (S)PME force error */
/* Determine the volume of the simulation box */
if (MASTER(cr))
{
info.volume = det(state.box);
calc_recipbox(state.box,info.recipbox);
info.natoms = mtop.natoms;
info.bTUNE = bTUNE;
}
if (PAR(cr))
bcast_info(&info, cr);
/* Get an error estimate of the input tpr file */
estimate_PME_error(&info, &state, &mtop, fp, cr);
if (MASTER(cr))
{
ir->ewald_rtol=info.ewald_rtol[0];
write_tpx_state(opt2fn("-so",NFILE,fnm),ir,&state,&mtop);
please_cite(fp,"Wang2010");
fclose(fp);
}
if (gmx_parallel_env_initialized())
{
gmx_finalize();
}
return 0;
}
int main(int argc,char *argv[])
{
static char *desc[] = {
"testlr tests the PPPM and Ewald method for the",
"long range electrostatics problem."
};
static t_filenm fnm[] = {
{ efTPX, NULL, NULL, ffREAD },
{ efHAT, "-g", "ghat", ffOPTRD },
{ efOUT, "-o", "rho", ffOPTWR },
{ efOUT, "-op", "lr-pb", ffOPTWR },
{ efOUT, "-of", "lr-four", ffOPTWR },
{ efOUT, "-opt", "tot-pb", ffOPTWR },
{ efOUT, "-oft", "tot-four", ffOPTWR },
{ efOUT, "-fin", "lr-four", ffOPTWR },
{ efEPS, "-es", "sr", ffOPTWR },
{ efEPS, "-elf", "lr-four", ffOPTWR },
{ efEPS, "-etf", "tot-four", ffOPTWR },
{ efEPS, "-qr", "qk-real", ffOPTWR },
{ efEPS, "-qi", "qk-im", ffOPTWR },
{ efEPS, "-elp", "lr-pb", ffOPTWR },
{ efEPS, "-etp", "tot-pb", ffOPTWR },
{ efEPS, "-rho", "rho", ffOPTWR },
{ efEPS, "-qq", "charge", ffOPTWR },
{ efXVG, "-gt", "gk-tab", ffOPTWR },
{ efXVG, "-fcorr","fcorr", ffWRITE },
{ efXVG, "-pcorr","pcorr", ffWRITE },
{ efXVG, "-ftotcorr","ftotcorr", ffWRITE },
{ efXVG, "-ptotcorr","ptotcorr", ffWRITE },
{ efLOG, "-l", "fptest", ffWRITE },
{ efXVG, "-gr", "spread", ffOPTWR },
{ efPDB, "-pf", "pqr-four", ffOPTWR },
{ efPDB, "-phitot", "pppm-phitot", ffOPTWR }
};
#define NFILE asize(fnm)
FILE *log;
t_topology top;
t_tpxheader stath;
t_inputrec ir;
t_block *excl;
t_forcerec *fr;
t_commrec *cr;
t_mdatoms *mdatoms;
t_graph *graph;
int i,step,nre,natoms,nmol;
rvec *x,*f_sr,*f_excl,*f_four,*f_pppm,*f_pois,box_size,hbox;
matrix box;
real t,lambda,vsr,*charge,*phi_f,*phi_pois,*phi_s,*phi_p3m,*rho;
static bool bFour=FALSE,bVerbose=FALSE,bGGhat=FALSE,bPPPM=TRUE,
bPoisson=FALSE,bOld=FALSE,bOldEwald=TRUE;
static int nprocs = 1;
static t_pargs pa[] = {
{ "-np", FALSE, etINT, &nprocs, "Do it in parallel" },
{ "-ewald", FALSE, etBOOL, &bFour, "Do an Ewald solution"},
{ "-pppm", FALSE, etBOOL, &bPPPM, "Do a PPPM solution" },
{ "-poisson",FALSE, etBOOL, &bPoisson,"Do a Poisson solution" },
{ "-v", FALSE, etBOOL, &bVerbose,"Verbose on"},
{ "-ghat", FALSE, etBOOL, &bGGhat, "Generate Ghat function"},
{ "-old", FALSE, etBOOL, &bOld, "Use old function types"},
{ "-oldewald",FALSE,etBOOL, &bOldEwald,"Use old Ewald code"}
};
CopyRight(stderr,argv[0]);
parse_common_args(&argc,argv,PCA_CAN_TIME | PCA_CAN_VIEW,
NFILE,fnm,asize(pa),pa,asize(desc),desc,0,NULL);
if (nprocs > 1) {
cr = init_par(&argc,argv);
open_log(ftp2fn(efLOG,NFILE,fnm),cr);
log = stdlog;
}
else {
cr = init_par(&argc,argv);
log = ftp2FILE(efLOG,NFILE,fnm,"w");
stdlog = log; }
/* Read topology and coordinates */
read_tpxheader(ftp2fn(efTPX,NFILE,fnm),&stath,FALSE);
snew(x,stath.natoms);
snew(f_sr,stath.natoms);
snew(f_excl,stath.natoms);
snew(f_four,stath.natoms);
snew(f_pppm,stath.natoms);
snew(f_pois,stath.natoms);
read_tpx(ftp2fn(efTPX,NFILE,fnm),&step,&t,&lambda,&ir,
box,&natoms,x,NULL,NULL,&top);
excl=&(top.atoms.excl);
nmol=top.blocks[ebMOLS].nr;
/* Allocate space for potential, charges and rho (charge density) */
snew(charge,stath.natoms);
snew(phi_f,stath.natoms);
snew(phi_p3m,stath.natoms);
snew(phi_pois,stath.natoms);
snew(phi_s,stath.natoms);
snew(rho,stath.natoms);
/* Set the charges */
for(i=0; (i<natoms); i++)
charge[i]=top.atoms.atom[i].q;
/* Make a simple box vector instead of tensor */
for(i=0; (i<DIM); i++)
box_size[i]=box[i][i];
/* Set some constants */
fr = mk_forcerec();
mdatoms = atoms2md(&(top.atoms),FALSE,FALSE);
set_LRconsts(log,ir.rcoulomb_switch,ir.rcoulomb,box_size,fr);
init_forcerec(log,fr,&ir,&(top.blocks[ebMOLS]),cr,
&(top.blocks[ebCGS]),&(top.idef),mdatoms,box,FALSE);
calc_shifts(box,box_size,fr->shift_vec,FALSE);
/* Periodicity stuff */
graph = mk_graph(&(top.idef),top.atoms.nr,FALSE,FALSE);
shift_self(graph,fr->shift_vec,x);
calc_LRcorrections(log,0,natoms,ir.rcoulomb_switch,
ir.rcoulomb,charge,excl,x,f_excl,bOld);
pr_f("f_excl.dat",natoms,f_excl);
/* Compute the short range potential */
put_atoms_in_box(natoms,box,x);
vsr=phi_sr(log,natoms,x,charge,ir.rcoulomb,
ir.rcoulomb_switch,box_size,phi_s,excl,f_sr,bOld);
pr_f("f_sr.dat",natoms,f_sr);
/* Plot the short range potential in a matrix */
calc_ener(log,"Short Range",TRUE,nmol,natoms,phi_s,charge,excl);
if (bFour)
test_four(log,NFILE,fnm,&(top.atoms),&ir,x,f_four,box_size,charge,phi_f,
phi_s,nmol,cr,bOld,bOldEwald);
if (bPPPM)
test_pppm(log,bVerbose,bGGhat,opt2fn("-g",NFILE,fnm),
&(top.atoms),&ir,x,f_pppm,charge,box_size,phi_p3m,phi_s,nmol,
cr,bOld,&(top.blocks[ebCGS]));
if (bPoisson)
test_poisson(log,bVerbose,
&(top.atoms),&ir,x,f_pois,charge,box_size,phi_pois,
phi_s,nmol,cr,bFour,f_four,phi_f,bOld);
if (bPPPM && bFour)
analyse_diff(log,"PPPM",
top.atoms.nr,f_four,f_pppm,phi_f,phi_p3m,phi_s,
opt2fn("-fcorr",NFILE,fnm),
opt2fn("-pcorr",NFILE,fnm),
opt2fn("-ftotcorr",NFILE,fnm),
opt2fn("-ptotcorr",NFILE,fnm));
if (bPoisson && bFour)
analyse_diff(log,"Poisson",
top.atoms.nr,f_four,f_pois,phi_f,phi_pois,phi_s,
opt2fn("-fcorr",NFILE,fnm),
opt2fn("-pcorr",NFILE,fnm),
opt2fn("-ftotcorr",NFILE,fnm),
opt2fn("-ptotcorr",NFILE,fnm));
gmx_fio_fclose(log);
thanx(stderr);
return 0;
}
int main(int argc,char *argv[])
{
static char *desc[] = {
"The ffscan program performs a single point energy and force calculation",
"in which the force field is modified. This way a range of parameters can",
"be changed and tested for reproduction of e.g. quantum chemical or",
"experimental data. A grid scan over the parameters is done as specified",
"using command line arguments. All parameters that reproduce the energy",
"within a given absolute tolerance are printed to a log file.[PAR]",
"Obviously polarizable models can be used, and shell optimisation is",
"performed if necessary. Also, like in [TT]mdrun[tt] table functions can be used",
"for user defined potential functions.[PAR]",
"If the option -ga with appropriate file is passed, a genetic algorithm will",
"be used rather than a grid scan."
};
t_commrec *cr;
static t_filenm fnm[] = {
{ efTPX, NULL, NULL, ffREAD },
{ efLOG, "-g", "md", ffWRITE },
{ efXVG, "-table", "table", ffOPTRD },
{ efDAT, "-parm", "params", ffREAD },
{ efDAT, "-ga", "genalg", ffOPTRD },
{ efGRO, "-c", "junk", ffWRITE },
{ efEDR, "-e", "junk", ffWRITE },
{ efTRN, "-o", "junk", ffWRITE }
};
#define NFILE asize(fnm)
/* Command line options ! */
static t_ffscan ff = {
/* tol */ 0.1,
/* f_max */ 100.0,
/* npow */ 12.0,
/* epot */ 0.0,
/* fac_epot */ 1.0,
/* fac_pres */ 0.1,
/* fac_msf */ 0.1,
/* pres */ 1.0,
/* molsize */ 1,
/* nmol */ 1,
/* bComb */ TRUE,
/* bVerbose */ FALSE,
/* bLogEps */ FALSE
};
static char *loadx=NULL,*loady=NULL,*loadz=NULL;
static t_pargs pa[] = {
{ "-tol", FALSE, etREAL, {&ff.tol}, "Energy tolerance (kJ/mol) (zero means everything is printed)" },
{ "-fmax", FALSE, etREAL, {&ff.f_max}, "Force tolerance (zero means everything is printed)" },
{ "-comb", FALSE, etBOOL, {&ff.bComb}, "Use combination rules" },
{ "-npow", FALSE, etREAL, {&ff.npow}, "Power for LJ in case of table use" },
{ "-logeps",FALSE, etBOOL, {&ff.bLogEps}, "Use a logarithmic scale for epsilon" },
{ "-v", FALSE, etBOOL, {&ff.bVerbose}, "Be loud and noisy" },
{ "-epot", FALSE, etREAL, {&ff.epot}, "Target energy (kJ/mol)" },
{ "-fepot", FALSE, etREAL, {&ff.fac_epot}, "Factor for scaling energy violations (0 turns energy contribution off)" },
{ "-pres", FALSE, etREAL, {&ff.pres}, "Value for reference pressure" },
{ "-fpres", FALSE, etREAL, {&ff.fac_pres}, "Factor for scaling pressure violations (0 turns pressure contribution off)" },
{ "-fmsf", FALSE, etREAL, {&ff.fac_msf}, "Factor for scaling mean square force violations (0 turns MSF contribution off)" },
{ "-molsize",FALSE,etINT, {&ff.molsize}, "Number of atoms per molecule" },
{ "-nmol", FALSE, etINT, {&ff.nmol}, "Number of molecules (Epot is divided by this value!)" }
};
#define NPA asize(pa)
unsigned long Flags = 0;
gmx_edsam_t ed=NULL;
FILE *fplog;
ivec ddxyz = { 1,1,1 };
cr = init_par(&argc,&argv);
ff.bVerbose = ff.bVerbose && MASTER(cr);
#if 0
snew(ed,1);
ed->eEDtype=eEDnone;
#endif
if (MASTER(cr))
CopyRight(stderr,argv[0]);
parse_common_args(&argc,argv,PCA_BE_NICE,NFILE,fnm,
NPA,pa,asize(desc),desc,0,NULL);
if (ff.npow <= 6.0)
gmx_fatal(FARGS,"Can not have repulsion with smaller exponent than 6");
if (ff.nmol < 1)
gmx_fatal(FARGS,"Can not fit %d molecules",ff.nmol);
gmx_log_open(ftp2fn(efLOG,NFILE,fnm),cr,FALSE,0,&fplog);
if (MASTER(cr)) {
CopyRight(fplog,argv[0]);
please_cite(fplog,"Lindahl2001a");
please_cite(fplog,"Berendsen95a");
}
set_ffvars(&ff);
Flags = (Flags | MD_FFSCAN);
mdrunner(fplog,cr,NFILE,fnm,ff.bVerbose,FALSE,
ddxyz,0,0,0,loadx,loady,loadz,1,
0,0,Flags);
if (gmx_parallel_env_initialized())
gmx_finalize(cr);
gmx_log_close(fplog);
return 0;
}
