#include <signal.h>
#include <stdlib.h>
#include "typedefs.h"
-#include "smalloc.h"
#include "sysstuff.h"
-#include "vec.h"
#include "statutil.h"
#include "macros.h"
#include "copyrite.h"
#include "main.h"
-#include "futil.h"
-#include "edsam.h"
-#include "checkpoint.h"
-#include "vcm.h"
-#include "mdebin.h"
-#include "nrnb.h"
-#include "calcmu.h"
-#include "index.h"
-#include "vsite.h"
-#include "update.h"
-#include "ns.h"
-#include "trnio.h"
-#include "xtcio.h"
-#include "mdrun.h"
-#include "confio.h"
-#include "network.h"
-#include "pull.h"
-#include "xvgr.h"
-#include "physics.h"
-#include "names.h"
-#include "disre.h"
-#include "orires.h"
-#include "dihre.h"
-#include "pppm.h"
-#include "pme.h"
-#include "mdatoms.h"
-#include "qmmm.h"
-#include "mpelogging.h"
-#include "domdec.h"
-#include "partdec.h"
-#include "topsort.h"
-#include "coulomb.h"
-#include "constr.h"
-#include "shellfc.h"
-#include "mvdata.h"
-#include "checkpoint.h"
-#include "mtop_util.h"
-#include "tpxio.h"
-#include "string2.h"
-#include "sighandler.h"
#include "gmx_ana.h"
#ifdef GMX_LIB_MPI
if (MASTER(cr))
{
- /* Update mdebin with energy history if appending to output files */
- if ( Flags & MD_APPENDFILES )
+ if (opt2bSet("-cpi",nfile,fnm))
{
- restore_energyhistory_from_state(mdebin,&state_global->enerhist);
+ /* Update mdebin with energy history if appending to output files */
+ if ( Flags & MD_APPENDFILES )
+ {
+ restore_energyhistory_from_state(mdebin,&state_global->enerhist);
+ }
+ else
+ {
+ /* We might have read an energy history from checkpoint,
+ * free the allocated memory and reset the counts.
+ */
+ done_energyhistory(&state_global->enerhist);
+ init_energyhistory(&state_global->enerhist);
+ }
}
- /* Set the initial energy history in state to zero by updating once */
+ /* Set the initial energy history in state by updating once */
update_energyhistory(&state_global->enerhist,mdebin);
}
return rc;
}
+
int gmx_membed(int argc,char *argv[])
{
const char *desc[] = {
" - It is recommended to perform a short equilibration run after the embedding",
"(see Wolf et al, J Comp Chem 31 (2010) 2169-2174, to re-equilibrate the membrane. Clearly",
"protein equilibration might require longer.\n",
+ " - It is now also possible to use the g_membed functionality with mdrun. You should than pass",
+ "a data file containing the command line options of g_membed following the -membed option, for",
+ "example mdrun -s into_mem.tpr -membed membed.dat.",
"\n"
};
- t_commrec *cr;
t_filenm fnm[] = {
{ efTPX, "-f", "into_mem", ffREAD },
{ efNDX, "-n", "index", ffOPTRD },
{ efTOP, "-p", "topol", ffOPTRW },
{ efTRN, "-o", NULL, ffWRITE },
{ efXTC, "-x", NULL, ffOPTWR },
- { efCPT, "-cpi", NULL, ffOPTRD },
- { efCPT, "-cpo", NULL, ffOPTWR },
{ efSTO, "-c", "membedded", ffWRITE },
{ efEDR, "-e", "ener", ffWRITE },
- { efLOG, "-g", "md", ffWRITE },
- { efEDI, "-ei", "sam", ffOPTRD },
- { efTRX, "-rerun", "rerun", ffOPTRD },
- { efXVG, "-table", "table", ffOPTRD },
- { efXVG, "-tablep", "tablep", ffOPTRD },
- { efXVG, "-tableb", "table", ffOPTRD },
- { efXVG, "-dhdl", "dhdl", ffOPTWR },
- { efXVG, "-field", "field", ffOPTWR },
- { efXVG, "-table", "table", 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 },
- { efMTX, "-mtx", "nm", ffOPTWR },
- { efNDX, "-dn", "dipole", ffOPTWR }
+ { efDAT, "-dat", "membed", ffWRITE }
};
#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,bAddPart=TRUE;
- gmx_bool bResetCountersHalfWay=FALSE;
- output_env_t oenv=NULL;
- const char *deviceOptions = "";
-
real xy_fac = 0.5;
real xy_max = 1.0;
real z_fac = 1.0;
int low_up_rm = 0;
int maxwarn=0;
int pieces=1;
- gmx_bool bALLOW_ASYMMETRY=FALSE;
-
+ gmx_bool bALLOW_ASYMMETRY=FALSE;
+ int nstepout=100;
+ gmx_bool bVerbose=FALSE;
+ char *mdrun_path=NULL;
/* arguments relevant to OPENMM only*/
#ifdef GMX_OPENMM
#endif
t_pargs pa[] = {
- { "-xyinit", FALSE, etREAL, {&xy_fac}, "Resize factor for the protein in the xy dimension before starting embedding" },
- { "-xyend", FALSE, etREAL, {&xy_max}, "Final resize factor in the xy dimension" },
- { "-zinit", FALSE, etREAL, {&z_fac}, "Resize factor for the protein in the z dimension before starting embedding" },
- { "-zend", FALSE, etREAL, {&z_max}, "Final resize faction in the z dimension" },
- { "-nxy", FALSE, etINT, {&it_xy}, "Number of iteration for the xy dimension" },
- { "-nz", FALSE, etINT, {&it_z}, "Number of iterations for the z dimension" },
- { "-rad", FALSE, etREAL, {&probe_rad}, "Probe radius to check for overlap between the group to embed and the membrane"},
- { "-pieces", FALSE, etINT, {&pieces}, "Perform piecewise resize. Select parts of the group to insert and resize these with respect to their own geometrical center." },
- { "-asymmetry",FALSE, etBOOL,{&bALLOW_ASYMMETRY}, "Allow asymmetric insertion, i.e. the number of lipids removed from the upper and lower leaflet will not be checked." },
- { "-ndiff" , FALSE, etINT, {&low_up_rm}, "Number of lipids that will additionally be removed from the lower (negative number) or upper (positive number) membrane leaflet." },
- { "-maxwarn", FALSE, etINT, {&maxwarn}, "Maximum number of warning allowed" },
- { "-pd", FALSE, etBOOL,{&bPartDec},
- "HIDDENUse particle decompostion" },
- { "-dd", FALSE, etRVEC,{&realddxyz},
- "HIDDENDomain decomposition grid, 0 is optimize" },
- { "-nt", FALSE, etINT, {&nthreads},
- "HIDDENNumber of threads to start (0 is guess)" },
- { "-npme", FALSE, etINT, {&npme},
- "HIDDENNumber of separate nodes to be used for PME, -1 is guess" },
- { "-ddorder", FALSE, etENUM, {ddno_opt},
- "HIDDENDD node order" },
- { "-ddcheck", FALSE, etBOOL, {&bDDBondCheck},
- "HIDDENCheck for all bonded interactions with DD" },
- { "-ddbondcomm", FALSE, etBOOL, {&bDDBondComm},
- "HIDDENUse special bonded atom communication when -rdd > cut-off" },
- { "-rdd", FALSE, etREAL, {&rdd},
- "HIDDENThe maximum distance for bonded interactions with DD (nm), 0 is determine from initial coordinates" },
- { "-rcon", FALSE, etREAL, {&rconstr},
- "HIDDENMaximum distance for P-LINCS (nm), 0 is estimate" },
- { "-dlb", FALSE, etENUM, {dddlb_opt},
- "HIDDENDynamic load balancing (with DD)" },
- { "-dds", FALSE, etREAL, {&dlb_scale},
- "HIDDENMinimum 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},
- "HIDDENGlobal communication frequency" },
- { "-compact", FALSE, etBOOL,{&bCompact},
- "Write a compact log file" },
- { "-seppot", FALSE, etBOOL, {&bSepPot},
- "HIDDENWrite separate V and dVdl terms for each interaction type and node to the log file(s)" },
- { "-pforce", FALSE, etREAL, {&pforce},
- "HIDDENPrint all forces larger than this (kJ/mol nm)" },
- { "-reprod", FALSE, etBOOL,{&bReproducible},
- "HIDDENTry to avoid optimizations that affect binary reproducibility" },
- { "-multi", FALSE, etINT,{&nmultisim},
- "HIDDENDo multiple simulations in parallel" },
- { "-replex", FALSE, etINT, {&repl_ex_nst},
- "HIDDENAttempt replica exchange every # steps" },
- { "-reseed", FALSE, etINT, {&repl_ex_seed},
- "HIDDENSeed for replica exchange, -1 is generate a seed" },
- { "-rerunvsite", FALSE, etBOOL, {&bRerunVSite},
- "HIDDENRecalculate virtual site coordinates with -rerun" },
- { "-ionize", FALSE, etBOOL,{&bIonize},
- "HIDDENDo a simulation including the effect of an X-Ray bombardment on your system" },
- { "-confout", TRUE, etBOOL, {&bConfout},
- "HIDDENWrite the last configuration with -c 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 -maxh" },
- { "-v", FALSE, etBOOL,{&bVerbose},
- "Be loud and noisy" },
- { "-maxh", FALSE, etREAL, {&max_hours},
- "HIDDENTerminate after 0.99 times this time (hours)" },
- { "-cpt", FALSE, etREAL, {&cpt_period},
- "HIDDENCheckpoint interval (minutes)" },
- { "-append", FALSE, etBOOL, {&bAppendFiles},
- "HIDDENAppend to previous output files when continuing from checkpoint" },
- { "-addpart", FALSE, etBOOL, {&bAddPart},
- "HIDDENAdd the simulation part number to all output files when continuing from checkpoint" },
+ { "-xyinit", FALSE, etREAL, {&xy_fac},
+ "Resize factor for the protein in the xy dimension before starting embedding" },
+ { "-xyend", FALSE, etREAL, {&xy_max},
+ "Final resize factor in the xy dimension" },
+ { "-zinit", FALSE, etREAL, {&z_fac},
+ "Resize factor for the protein in the z dimension before starting embedding" },
+ { "-zend", FALSE, etREAL, {&z_max},
+ "Final resize faction in the z dimension" },
+ { "-nxy", FALSE, etINT, {&it_xy},
+ "Number of iteration for the xy dimension" },
+ { "-nz", FALSE, etINT, {&it_z},
+ "Number of iterations for the z dimension" },
+ { "-rad", FALSE, etREAL, {&probe_rad},
+ "Probe radius to check for overlap between the group to embed and the membrane"},
+ { "-pieces", FALSE, etINT, {&pieces},
+ "Perform piecewise resize. Select parts of the group to insert and resize these with respect to their own geometrical center." },
+ { "-asymmetry",FALSE, etBOOL,{&bALLOW_ASYMMETRY},
+ "Allow asymmetric insertion, i.e. the number of lipids removed from the upper and lower leaflet will not be checked." },
+ { "-ndiff" , FALSE, etINT, {&low_up_rm},
+ "Number of lipids that will additionally be removed from the lower (negative number) or upper (positive number) membrane leaflet." },
+ { "-maxwarn", FALSE, etINT, {&maxwarn},
+ "Maximum number of warning allowed" },
+ { "-stepout", FALSE, etINT, {&nstepout},
+ "HIDDENFrequency of writing the remaining runtime" },
+ { "-v", FALSE, etBOOL,{&bVerbose},
+ "Be loud and noisy" },
+ { "-mdrun_path", FALSE, etSTR, {&mdrun_path},
+ "Path to the mdrun executable compiled with this g_membed version" }
};
- gmx_edsam_t ed;
- unsigned long Flags, PCA_Flags;
- ivec ddxyz;
- int dd_node_order;
- gmx_bool HaveCheckpoint;
- FILE *fplog,*fptest;
- int sim_part,sim_part_fn;
- const char *part_suffix=".part";
- char suffix[STRLEN];
- int rc;
-
-
- cr = init_par(&argc,&argv);
-
- 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;
-#ifdef GMX_THREADS
- /* now determine the number of threads automatically. The threads are
- only started at mdrunner_threads, though. */
- if (nthreads<1)
- {
- nthreads=tMPI_Get_recommended_nthreads();
- }
-#else
- nthreads=1;
-#endif
+ FILE *data_out;
+ output_env_t oenv;
+ char buf[256],buf2[64];
- if (repl_ex_nst != 0 && nmultisim < 2)
- gmx_fatal(FARGS,"Need at least two replicas for replica exchange (option -multi)");
+ parse_common_args(&argc,argv,0, NFILE,fnm,asize(pa),pa,
+ asize(desc),desc,0,NULL, &oenv);
- if (nmultisim > 1) {
-#ifndef GMX_THREADS
- init_multisystem(cr,nmultisim,NFILE,fnm,TRUE);
-#else
- gmx_fatal(FARGS,"mdrun -multi is not supported with the thread library.Please compile GROMACS with MPI support");
-#endif
- }
+ data_out = ffopen(opt2fn("-dat",NFILE,fnm),"w");
+ fprintf(data_out,"nxy = %d\nnz = %d\nxyinit = %f\nxyend = %f\nzinit = %f\nzend = %f\n"
+ "rad = %f\npieces = %d\nasymmetry = %s\nndiff = %d\nmaxwarn = %d\n",
+ it_xy,it_z,xy_fac,xy_max,z_fac,z_max,probe_rad,pieces,
+ bALLOW_ASYMMETRY ? "yes" : "no",low_up_rm,maxwarn);
+ fclose(data_out);
- /* Check if there is ANY checkpoint file available */
- sim_part = 1;
- sim_part_fn = sim_part;
- if (opt2bSet("-cpi",NFILE,fnm))
- {
- 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;
- }
- }
- else
+ sprintf(buf,"%s -s %s -membed %s -o %s -c %s -e %s -nt 1 -cpt -1",
+ (mdrun_path==NULL) ? "mdrun" : mdrun_path,
+ opt2fn("-f",NFILE,fnm),opt2fn("-dat",NFILE,fnm),opt2fn("-o",NFILE,fnm),
+ opt2fn("-c",NFILE,fnm),opt2fn("-e",NFILE,fnm));
+ if (opt2bSet("-n",NFILE,fnm))
{
- bAppendFiles = FALSE;
- }
-
- if (!bAppendFiles)
- {
- sim_part_fn = sim_part;
- }
-
- if (bAddPart && sim_part_fn > 1)
- {
- /* This is a continuation run, rename trajectory 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);
- 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 | (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 | (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)
+ sprintf(buf2," -mn %s",opt2fn("-n",NFILE,fnm));
+ strcat(buf,buf2);
+ }
+ if (opt2bSet("-x",NFILE,fnm))
{
- 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");
+ sprintf(buf2," -x %s",opt2fn("-x",NFILE,fnm));
+ strcat(buf,buf2);
}
- else
+ if (opt2bSet("-p",NFILE,fnm))
+ {
+ sprintf(buf2," -mp %s",opt2fn("-p",NFILE,fnm));
+ strcat(buf,buf2);
+ }
+ if (bVerbose)
{
- fplog = NULL;
+ sprintf(buf2," -v -stepout %d",nstepout);
+ strcat(buf,buf2);
}
- ddxyz[XX] = (int)(realddxyz[XX] + 0.5);
- ddxyz[YY] = (int)(realddxyz[YY] + 0.5);
- ddxyz[ZZ] = (int)(realddxyz[ZZ] + 0.5);
-
- /* even if nthreads = 1, we still call this one */
-
- rc = mdrunner_membed(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,
- xy_fac,xy_max,z_fac,z_max,
- it_xy,it_z,probe_rad,low_up_rm,
- pieces,bALLOW_ASYMMETRY,maxwarn);
+ printf("%s\n",buf);
+ system(buf);
- 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) */
- fprintf(stderr,"Please cite:\nWolf et al, J Comp Chem 31 (2010) 2169-2174.\n");
-
- if (MASTER(cr) && !bAppendFiles)
- {
- gmx_log_close(fplog);
- }
+ fprintf(stderr,"Please cite:\nWolf et al, J Comp Chem 31 (2010) 2169-2174.\n");
- return rc;
+ return 0;
}
biod.pnpi.spb.ru / alexxy / gromacs.git / commitdiff