--- /dev/null
+/*
+ *
+ * This source code is part of
+ *
+ * G R O M A C S
+ *
+ * GROningen MAchine for Chemical Simulations
+ *
+ * VERSION 3.2.0
+ * Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
+ * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
+ * Copyright (c) 2001-2004, 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
+ *
+ * And Hey:
+ * Green Red Orange Magenta Azure Cyan Skyblue
+ */
+
+#ifdef HAVE_CONFIG_H
+#include <config.h>
+#endif
+
+#include <math.h>
+#include <ctype.h>
+#include "string2.h"
+#include "sysstuff.h"
+#include "typedefs.h"
+#include "macros.h"
+#include "vec.h"
+#include "pbc.h"
+#include "xvgr.h"
+#include "copyrite.h"
+#include "futil.h"
+#include "statutil.h"
+#include "tpxio.h"
+#include "physics.h"
+#include "index.h"
+#include "smalloc.h"
+#include "calcgrid.h"
+#include "nrnb.h"
+#include "coulomb.h"
+#include "gstat.h"
+#include "matio.h"
+#include "strdb.h"
+#include "gmx_ana.h"
+#include "names.h"
+#include "gmx_random.h"
+
+/*
+ * This part will be organized as part of gmxlib in nsfactor.c in near future
+ */
+
+typedef struct gmx_nstructurefactors {
+ int nratoms;
+ int *p; /* proton number */
+ int *n; /* neuton number */
+ double *slength; /* scattering length in fm */
+ char **atomnm; /* atom symbol */
+} gmx_nstructurefactors;
+
+typedef struct gmx_sans_t {
+ t_topology *top; /* topology */
+ double *slength; /* scattering length for this topology */
+} gmx_sans_t;
+
+typedef struct gmx_gr_t {
+ int grn; /* number of bins */
+ double binwidth; /* bin size */
+ double *r; /* Distances */
+ double *gr; /* Probability */
+} gmx_gr_t;
+
+typedef struct gmx_sq_t {
+ int qn; /* number of items */
+ double *s; /* scattering */
+ double *q; /* q vectors */
+ double qstep; /* q increment */
+} gmx_sq_t;
+
+void normalize_probability(int n,double *a){
+ int i;
+ double norm=0.0;
+ for (i=0;i<n;i++) norm +=a[i];
+ for (i=0;i<n;i++) a[i]/=norm;
+}
+
+extern gmx_nstructurefactors *gmx_structurefactors_init(const char *datfn) {
+ /* read nsfactor.dat */
+ FILE *fp;
+ char line[STRLEN];
+ int nralloc=10;
+ int n,p;
+ int i, line_no;
+ char atomnm[8];
+ double slength;
+ gmx_nstructurefactors *gnsf;
+
+ fp=libopen(datfn);
+ line_no = 0;
+ /* allocate memory for structure */
+ snew(gnsf,nralloc);
+ snew(gnsf->atomnm,nralloc);
+ snew(gnsf->p,nralloc);
+ snew(gnsf->n,nralloc);
+ snew(gnsf->slength,nralloc);
+
+ gnsf->nratoms=line_no;
+
+ while(get_a_line(fp,line,STRLEN)) {
+ i=line_no;
+ if (sscanf(line,"%s %d %d %lf",atomnm,&p,&n,&slength) == 4) {
+ gnsf->atomnm[i]=strdup(atomnm);
+ gnsf->n[i]=n;
+ gnsf->p[i]=p;
+ gnsf->slength[i]=slength;
+ line_no++;
+ gnsf->nratoms=line_no;
+ if (line_no==nralloc){
+ nralloc++;
+ srenew(gnsf->atomnm,nralloc);
+ srenew(gnsf->p,nralloc);
+ srenew(gnsf->n,nralloc);
+ srenew(gnsf->slength,nralloc);
+ }
+ } else
+ fprintf(stderr,"WARNING: Error in file %s at line %d ignored\n",
+ datfn,line_no);
+ }
+ srenew(gnsf->atomnm,gnsf->nratoms);
+ srenew(gnsf->p,gnsf->nratoms);
+ srenew(gnsf->n,gnsf->nratoms);
+ srenew(gnsf->slength,gnsf->nratoms);
+
+ fclose(fp);
+
+ return (gmx_nstructurefactors *) gnsf;
+}
+
+extern gmx_sans_t *gmx_sans_init (t_topology *top, gmx_nstructurefactors *gnsf) {
+ gmx_sans_t *gsans=NULL;
+ int i,j;
+ /* Try to assing scattering length from nsfactor.dat */
+ snew(gsans,1);
+ snew(gsans->slength,top->atoms.nr);
+ /* copy topology data */
+ gsans->top = top;
+ for(i=0;i<top->atoms.nr;i++) {
+ for(j=0;j<gnsf->nratoms;j++) {
+ if(top->atoms.atom[i].atomnumber == gnsf->p[j]) {
+ /* we need special case for H and D */
+ if(top->atoms.atom[i].atomnumber == 1) {
+ if(top->atoms.atom[i].m == 1.008000) {
+ gsans->slength[i] = gnsf->slength[0];
+ } else
+ gsans->slength[i] = gnsf->slength[1];
+ } else
+ gsans->slength[i] = gnsf->slength[j];
+ }
+ }
+ }
+
+ return (gmx_sans_t *) gsans;
+}
+
+extern gmx_gr_t *calc_pr (gmx_sans_t *gsans, rvec *x, atom_id *index, int isize, double binwidth, gmx_bool bMC, gmx_large_int_t nmc, unsigned int seed) {
+ gmx_gr_t *pr=NULL;
+ rvec xmin, xmax;
+ double rmax;
+ int i,j,d;
+ int mc;
+ gmx_rng_t rng=NULL;
+
+ /* allocate memory for pr */
+ snew(pr,1);
+ /* set some fields */
+ pr->binwidth=binwidth;
+
+ /* Lets try to find min and max distance */
+ for(d=0;d<3;d++) {
+ xmax[d]=x[index[0]][d];
+ xmin[d]=x[index[0]][d];
+ }
+
+ for(i=1;i<isize;i++)
+ for(d=0;d<3;d++)
+ if (xmax[d]<x[index[i]][d]) xmax[d]=x[index[i]][d]; else
+ if (xmin[d]>x[index[i]][d]) xmin[d]=x[index[i]][d];
+
+ rmax=sqrt(distance2(xmax,xmin));
+
+ pr->grn=(int)floor(rmax/pr->binwidth)+1;
+ rmax=pr->grn*pr->binwidth;
+
+ snew(pr->gr,pr->grn);
+
+ if(bMC) {
+ /* Use several independent mc runs to collect better statistics */
+ for(d=0;d<(int)floor(nmc/524288);d++) {
+ rng=gmx_rng_init(seed);
+ for(mc=0;mc<524288;mc++) {
+ i=(int)floor(gmx_rng_uniform_real(rng)*isize);
+ j=(int)floor(gmx_rng_uniform_real(rng)*isize);
+ if(i!=j)
+ pr->gr[(int)floor(sqrt(distance2(x[index[i]],x[index[j]]))/binwidth)]+=gsans->slength[index[i]]*gsans->slength[index[j]];
+ }
+ gmx_rng_destroy(rng);
+ }
+ } else {
+ for(i=0;i<isize;i++)
+ for(j=0;j<i;j++)
+ pr->gr[(int)floor(sqrt(distance2(x[index[i]],x[index[j]]))/binwidth)]+=gsans->slength[index[i]]*gsans->slength[index[j]];
+ }
+
+ /* normalize */
+ normalize_probability(pr->grn,pr->gr);
+ snew(pr->r,pr->grn);
+ for(i=0;i<pr->grn;i++)
+ pr->r[i]=(pr->binwidth*i+pr->binwidth*0.5);
+
+ return (gmx_gr_t *) pr;
+}
+
+extern gmx_sq_t *pr2iq (gmx_gr_t *pr, double start_q, double end_q, double q_step) {
+ gmx_sq_t *sq=NULL;
+ int i,j;
+ /* init data */
+ snew(sq,1);
+ sq->qn=(int)floor((end_q-start_q)/q_step);
+ snew(sq->q,sq->qn);
+ snew(sq->s,sq->qn);
+ for(i=0;i<sq->qn;i++)
+ sq->q[i]=start_q+i*q_step;
+
+ if(start_q==0.0) {
+ sq->s[0]=1.0;
+ for(i=1;i<sq->qn;i++) {
+ for(j=0;j<pr->grn;j++)
+ sq->s[i]+=(pr->gr[j]/pr->r[j])*sin(sq->q[i]*pr->r[j]);
+ sq->s[i] /= sq->q[i];
+ }
+ } else {
+ for(i=0;i<sq->qn;i++) {
+ for(j=0;j<pr->grn;j++)
+ sq->s[i]+=(pr->gr[j]/pr->r[j])*sin(sq->q[i]*pr->r[j]);
+ sq->s[i] /= sq->q[i];
+ }
+ }
+
+ return (gmx_sq_t *) sq;
+}
+
+int gmx_sans(int argc,char *argv[])
+{
+ const char *desc[] = {
+ "This is simple tool to compute SANS spectra using Debye formula",
+ "It currently uses topology file (since it need to assigne element for each atom)",
+ "[PAR]",
+ "[TT]-pr[TT] Computes normalized g(r) function",
+ "[PAR]",
+ "[TT]-sq[TT] Computes SANS intensity curve for needed q diapason",
+ "[PAR]",
+ "[TT]-startq[TT] Starting q value in nm",
+ "[PAR]",
+ "[TT]-endq[TT] Ending q value in nm",
+ "[PAR]",
+ "[TT]-qstep[TT] Stepping in q space",
+ "[PAR]",
+ "Note: When using Debye direct method computational cost increases as",
+ "1/2 * N * (N - 1) where N is atom number in group of interest"
+ };
+ static gmx_bool bPBC=TRUE;
+ static real binwidth=0.2,grid=0.05; /* bins shouldnt be smaller then bond (~0.1nm) length */
+ static real start_q=0.0, end_q=2.0, q_step=0.01;
+ static gmx_large_int_t nmc=1048576;
+ static unsigned int seed=0;
+
+ static const char *emode[]= { NULL, "direct", "mc", NULL };
+ static const char *emethod[]={ NULL, "debye", "fft", NULL };
+
+ gmx_nstructurefactors *gnsf;
+ gmx_sans_t *gsans;
+
+#define NPA asize(pa)
+
+ t_pargs pa[] = {
+ { "-bin", FALSE, etREAL, {&binwidth},
+ "[HIDDEN]Binwidth (nm)" },
+ { "-mode", FALSE, etENUM, {emode},
+ "Mode for sans spectra calculation" },
+ { "-nmc", FALSE, etINT, {&nmc},
+ "Number of iterations for Monte-Carlo run"},
+ { "-method", FALSE, etENUM, {emethod},
+ "[HIDDEN]Method for sans spectra calculation" },
+ { "-pbc", FALSE, etBOOL, {&bPBC},
+ "Use periodic boundary conditions for computing distances" },
+ { "-grid", FALSE, etREAL, {&grid},
+ "[HIDDEN]Grid spacing (in nm) for FFTs" },
+ {"-startq", FALSE, etREAL, {&start_q},
+ "Starting q (1/nm) "},
+ {"-endq", FALSE, etREAL, {&end_q},
+ "Ending q (1/nm)"},
+ { "-qstep", FALSE, etREAL, {&q_step},
+ "Stepping in q (1/nm)"},
+ { "-seed", FALSE, etINT, {&seed},
+ "Random seed for Monte-Carlo"},
+ };
+ FILE *fp;
+ const char *fnTPX,*fnNDX,*fnDAT=NULL;
+ t_trxstatus *status;
+ t_topology *top=NULL;
+ t_atom *atom=NULL;
+ gmx_rmpbc_t gpbc=NULL;
+ gmx_bool bTPX;
+ gmx_bool bFFT=FALSE, bDEBYE=FALSE;
+ gmx_bool bMC=FALSE, bDIRECT=FALSE;
+ int ePBC=-1;
+ matrix box;
+ char title[STRLEN];
+ rvec *x;
+ int natoms;
+ real t;
+ char **grpname=NULL;
+ atom_id *index=NULL;
+ int isize;
+ int i,j;
+ gmx_gr_t *pr=NULL;
+ gmx_sq_t *sq=NULL;
+ output_env_t oenv;
+
+#define NFILE asize(fnm)
+
+ t_filenm fnm[] = {
+ { efTPX, "-s", NULL, ffREAD },
+ { efNDX, NULL, NULL, ffOPTRD },
+ { efDAT, "-d", "nsfactor", ffOPTRD },
+ { efXVG, "-sq", "sq", ffWRITE },
+ { efXVG, "-pr", "pr", ffWRITE }
+ };
+
+ CopyRight(stderr,argv[0]);
+ parse_common_args(&argc,argv,PCA_BE_NICE,
+ NFILE,fnm,asize(pa),pa,asize(desc),desc,0,NULL,&oenv);
+
+ /* Now try to parse opts for modes */
+ switch(emethod[0][0]) {
+ case 'd':
+ bDEBYE=TRUE;
+ switch(emode[0][0]) {
+ case 'd':
+ bDIRECT=TRUE;
+ fprintf(stderr,"Using direct Debye method to calculate spectrum\n");
+ break;
+ case 'm':
+ bMC=TRUE;
+ fprintf(stderr,"Using Monte Carlo Debye method to calculate spectrum\n");
+ break;
+ default:
+ break;
+ }
+ break;
+ case 'f':
+ bFFT=TRUE;
+ fprintf(stderr,"Using FFT method\n");
+ break;
+ default:
+ break;
+ }
+
+ if (!bDEBYE && !bFFT)
+ gmx_fatal(FARGS,"Unknown method. Set pr or fft!\n");
+ if (!bDIRECT && !bMC)
+ gmx_fatal(FARGS,"Unknown mode for g(r) method set to direct or mc!");
+ /* Try to read files */
+ fnDAT = ftp2fn(efDAT,NFILE,fnm);
+ fnTPX = ftp2fn(efTPX,NFILE,fnm);
+
+ gnsf = gmx_structurefactors_init(fnDAT);
+ fprintf(stderr,"Read %d atom names from %s with neutron scattering parameters\n\n",gnsf->nratoms,fnDAT);
+
+ snew(top,1);
+ snew(grpname,1);
+ snew(index,1);
+
+ bTPX=read_tps_conf(fnTPX,title,top,&ePBC,&x,NULL,box,TRUE);
+
+ printf("\nPlease select group for SANS spectra calculation:\n");
+ get_index(&(top->atoms),ftp2fn_null(efNDX,NFILE,fnm),1,&isize,&index,grpname);
+
+ gsans = gmx_sans_init(top,gnsf);
+
+ /* Prepare reference frame */
+ if (bPBC) {
+ gpbc = gmx_rmpbc_init(&top->idef,ePBC,top->atoms.nr,box);
+ gmx_rmpbc(gpbc,top->atoms.nr,box,x);
+ }
+
+ natoms=top->atoms.nr;
+ if (bDEBYE) {
+ if (bDIRECT) {
+ /* calc pr */
+ pr = calc_pr(gsans,x,index,isize,binwidth,bMC,nmc,seed);
+ } else if (bMC) {
+ if (nmc>(gmx_large_int_t)floor(0.5*isize*(isize-1))) {
+ fprintf(stderr,"Number of mc iteration larger then number of pairs in index group. Switching to direct method!\n");
+ bMC=FALSE;
+ bDIRECT=TRUE;
+ pr = calc_pr(gsans,x,index,isize,binwidth,bMC,nmc,seed);
+ } else {
+ pr = calc_pr(gsans,x,index,isize,binwidth,bMC,nmc,seed);
+ }
+ } else {
+ gmx_fatal(FARGS,"Unknown method!\n");
+ }
+ } else if (bFFT) {
+ gmx_fatal(FARGS,"Not implented!\n");
+ } else {
+ gmx_fatal(FARGS,"Whats this!?\n");
+ }
+
+ /* prepare pr.xvg */
+ fp = xvgropen(opt2fn_null("-pr",NFILE,fnm),"G(r)","Distance (nm)","Probability",oenv);
+ for(i=0;i<pr->grn;i++)
+ fprintf(fp,"%10.6lf%10.6lf\n",pr->r[i],pr->gr[i]);
+ fclose(fp);
+
+ /* prepare sq.xvg */
+ sq = pr2iq(pr,start_q,end_q,q_step);
+ fp = xvgropen(opt2fn_null("-sq",NFILE,fnm),"I(q)","q (nm^-1)","s(q)/s(0)",oenv);
+ for(i=0;i<sq->qn;i++) {
+ fprintf(fp,"%10.6lf%10.6lf\n",sq->q[i],sq->s[i]);
+ }
+ fclose(fp);
+
+ sfree(pr);
+
+ thanx(stderr);
+
+ return 0;
+}
biod.pnpi.spb.ru / alexxy / gromacs.git / commitdiff