how to use gromacs 4.5.5's temple Dear teacher, i have already modify the code, and also make it. Attached is my modified code good. >> Dear teacher, >> how to use gromacs 4.5.5's temple? > >I expect that it is not meant to be functional. It's meant to be a >template from which you can write functional code without having to work >too hard on making it work like GROMACS tools work. > >Mark > >> i make the temple successful! And when i run it (./template -f traj.xtc -s water.tpr -cutoff 2), the output like this:
" Reading file water.tpr, VERSION 4.5.5 (single precision) Reading file water.tpr, VERSION 4.5.5 (single precision) Specify a reference selection: (one selection per line, 'help' for help) > help SELECTION HELP This program supports selections in addition to traditional index files. Please read the subtopic pages (available through "help topic") for more information. Explanation of command-line arguments for specifying selections can be found under the "cmdline" subtopic, and general selection syntax is described under "syntax". Available keywords can be found under "keywords", and concrete examples under "examples". Other subtopics give more details on certain aspects. "help all" prints the help for all subtopics. Available subtopics: cmdline syntax positions arithmetic keywords evaluation limitations examples > " thanks!! Regards, Bodu Department of Polymer Science and Engineering, School of Chemical Engineering and technology, Tianjin University, Weijin Road 92, Nankai District 300072, Tianjin City P. R. China Tel/Fax: +86-22-27404303 ; +8613820062885 E-mail: 2008d...@gmail.com ; dubo2...@tju.edu.cn
/* * * This source code is part of * * G R O M A C S * * GROningen MAchine for Chemical Simulations * * Written by David van der Spoel, Erik Lindahl, Berk Hess, and others. * Copyright (c) 1991-2000, University of Groningen, The Netherlands. * Copyright (c) 2001-2009, The GROMACS development team, * check out http://www.gromacs.org for more information. * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License * as published by the Free Software Foundation; either version 2 * of the License, or (at your option) any later version. * * If you want to redistribute modifications, please consider that * scientific software is very special. Version control is crucial - * bugs must be traceable. We will be happy to consider code for * inclusion in the official distribution, but derived work must not * be called official GROMACS. Details are found in the README & COPYING * files - if they are missing, get the official version at www.gromacs.org. * * To help us fund GROMACS development, we humbly ask that you cite * the papers on the package - you can find them in the top README file. * * For more info, check our website at http://www.gromacs.org */ #include <gromacs/copyrite.h> #include <gromacs/filenm.h> #include <gromacs/macros.h> #include <gromacs/pbc.h> #include <gromacs/smalloc.h> #include <gromacs/statutil.h> #include <gromacs/vec.h> #include <gromacs/xvgr.h> #include <gromacs/nbsearch.h> #include <gromacs/trajana.h> #define ATOMS 1000 #define ATOMS 1000 #define BIN 1000 /*! \brief * Template analysis data structure. */ typedef struct { gmx_ana_selection_t *refsel; FILE *fp; real *ave; real *n; gmx_ana_nbsearch_t *nb; real dibond[ATOMS][ATOMS][BIN]; int nbin; int natoms; real cutoff; } t_analysisdata; /*! \brief * Function that does the analysis for a single frame. * * It is called once for each frame. */ static int analyze_frame(t_topology *top, t_trxframe *fr, t_pbc *pbc, int nr, gmx_ana_selection_t *sel[], void *data) { t_analysisdata *d = (t_analysisdata *)data; int g, i,j,bin,m; real frave,distance; int rc; d->natoms=fr->natoms; /* Here, you can do whatever analysis your program requires for a frame. */ //===============edit by bodu 2011-12-25 for (i=0;i<fr->natoms;i++) for (j=i+1;j<fr->natoms;j++) for (m=0;m<d->nbin;m++) d->dibond[i][j][m]=0.0; for (i=0;i<fr->natoms;i++) for (j=i+1;j<fr->natoms;j++){ distance=sqrt((fr->x[i][0]-fr->x[j][0])*(fr->x[i][0]-fr->x[j][0])+(fr->x[i][1]-fr->x[j][1])*(fr->x[i][1]-fr->x[j][1])+(fr->x[i][2]-fr->x[j][2])*(fr->x[i][2]-fr->x[j][2])); bin=(int)(distance/(d->cutoff/(d->nbin*1.0))); d->dibond[i][j][bin]++; } //======end======edit by bodu 2011-12-25 if (d->fp) { fprintf(d->fp, "%10.3f", fr->time); } rc = gmx_ana_nbsearch_pos_init(d->nb, pbc, &d->refsel->p); if (rc != 0) { gmx_fatal(FARGS, "Neighborhood search initialization failed"); } for (g = 0; g < nr; ++g) { frave = 0; for (i = 0; i < sel[g]->p.nr; ++i) { frave += gmx_ana_nbsearch_pos_mindist(d->nb, &sel[g]->p, i); } d->ave[g] += frave; d->n[g] += sel[g]->p.nr; if (d->fp) { frave /= sel[g]->p.nr; fprintf(d->fp, " %.3f", frave); } } if (d->fp) { fprintf(d->fp, "\n"); } /* We need to return 0 to tell that everything went OK */ return 0; } /*! \brief * Function that implements the analysis tool. * * Following the style of Gromacs analysis tools, this function is called * \p gmx_something. */ int gmx_template(int argc, char *argv[]) { const char *desc[] = { "This is a template for writing your own analysis tools for", "Gromacs. The advantage of using Gromacs for this is that you", "have access to all information in the topology, and your", "program will be able to handle all types of coordinates and", "trajectory files supported by Gromacs. In addition,", "you get a lot of functionality for free from the trajectory", "analysis library, including support for flexible dynamic", "selections. Go ahead an try it![PAR]", "To get started with implementing your own analysis program,", "follow the instructions in the README file provided.", "This template implements a simple analysis programs that calculates", "average distances from the a reference group to one or more", "analysis groups.", }; /* Command-line arguments */ real cutoff = 0; gmx_bool bArg = FALSE; t_pargs pa[] = { {"-cutoff", FALSE, etREAL, {&cutoff}, "Cutoff for distance calculation (0 = no cutoff)"}, {"-arg2", FALSE, etBOOL, {&bArg}, "Example argument 2"}, }; /* The second argument is for demonstration purposes only */ /* Output files */ t_filenm fnm[] = { {efXVG, "-o", "avedist", ffOPTWR}, }; #define NFILE asize(fnm) gmx_ana_traj_t *trj; output_env_t oenv; t_analysisdata d; int ngrps; gmx_ana_selection_t **sel; int g; int rc; printf("\n Please input the nbin:\n"); scanf("%d",&d.nbin); CopyRight(stderr, argv[0]); /* Here, we can use flags to specify requirements for the selections and/or * other features of the library. */ gmx_ana_traj_create(&trj, ANA_REQUIRE_TOP); gmx_ana_set_nrefgrps(trj, 1); gmx_ana_set_nanagrps(trj, -1); /* If required, other functions can also be used to configure the library * before calling parse_trjana_args(). */ parse_trjana_args(trj, &argc, argv, PCA_CAN_VIEW, NFILE, fnm, asize(pa), pa, asize(desc), desc, 0, NULL, &oenv); /* You can now do any initialization you wish, using the information * from the trj structure. * In particular, you should store any command-line parameter values that * the analysis part requires into d for them to be accessible. */ /* First, we get some selection information from the structure */ //gmx_ana_get_refsel(trj, 0, &d.refsel); //gmx_ana_get_nanagrps(trj, &ngrps); //gmx_ana_get_anagrps(trj, &sel); ///* First, we initialize the neighborhood search for the first index // * group. */ //rc = gmx_ana_nbsearch_create(&d.nb, cutoff, d.refsel->p.nr); //if (rc != 0) //{ // gmx_fatal(FARGS, "neighborhood search initialization failed"); //} ///* We then allocate memory in d to store intermediate data // * and initialize the counters to zero */ //snew(d.ave, ngrps); //snew(d.n, ngrps); ///* We also open the output file if the user provided it */ //d.fp = NULL; //if (opt2bSet("-o", NFILE, fnm)) //{ // d.fp = xvgropen(opt2fn("-o", NFILE, fnm), "Average distance", // "Time [ps]", "Distance [nm]", oenv); // xvgr_selections(d.fp, trj); //} d.cutoff=cutoff; /* Now, we do the actual analysis */ gmx_ana_do(trj, 0, &analyze_frame, &d); /* Now, the analysis has been done for all frames, and you can access the * results in d. Here, you should post-process your data and write out any * averaged properties. */ /* For the template, we close the output file if one was opened */ if (d.fp) { ffclose(d.fp); } /* We also calculate the average distance for each group */ for (g = 0; g < ngrps; ++g) { d.ave[g] /= d.n[g]; fprintf(stderr, "Average distance for '%s': %.3f nm\n", sel[g]->name, d.ave[g]); } //======output=========edit by bodu 2011-12-25 char newfilename[100]; char *filename; int i,j,file_number1,file_number2,m; filename=newfilename; FILE *fp; for (i=0;i<d.natoms;i++) for (j=i+1;j<d.natoms;j++) for (m=0;m<d.nbin;m++){ sprintf(filename,"total_%d_%d.xvg",(i+1),(j+1)); fp=fopen(filename,"a+"); fprintf(fp, "%.3f %.3f\n", m*(d.cutoff/(d.nbin*1.0)), d.dibond[i][j][m]); fclose(fp); } //======end======edit by bodu 2011-12-25 /* Here, we could free some memory, but this usually not necessary as we * are going to quit anyways. */ thanx(stderr); return 0; } /*! \brief * The main function. * * In Gromacs, most analysis programs are implemented such that the \p main * function is only a wrapper for a \p gmx_something function that does all * the work, and that convention is also followed here. */ int main(int argc, char *argv[]) { gmx_template(argc, argv); return 0; }
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