-/* -*- mode: c; tab-width: 4; indent-tabs-mode: nil; c-basic-offset: 4; c-file-style: "stroustrup"; -*-
+/*
+ * This file is part of the GROMACS molecular simulation package.
*
- *
- * 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
+ * Copyright (c) 2001-2004, The GROMACS development team.
+ * Copyright (c) 2012,2014, by the GROMACS development team, led by
+ * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+ * and including many others, as listed in the AUTHORS file in the
+ * top-level source directory and at http://www.gromacs.org.
+ *
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* of the License, or (at your option) any later version.
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* 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.
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*/
/* This file is completely threadsafe - keep it that way! */
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
#include <math.h>
#include <string.h>
-#include "sysstuff.h"
-#include "smalloc.h"
-#include "typedefs.h"
-#include "gmx_fatal.h"
-#include "string2.h"
-#include "ebin.h"
-#include "main.h"
-#include "maths.h"
-#include "vec.h"
-#include "physics.h"
+#include "gromacs/utility/smalloc.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/legacyheaders/ebin.h"
+#include "gromacs/math/utilities.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/math/units.h"
t_ebin *mk_ebin(void)
{
- t_ebin *eb;
-
- snew(eb,1);
-
- return eb;
+ t_ebin *eb;
+
+ snew(eb, 1);
+
+ return eb;
}
-int get_ebin_space(t_ebin *eb,int nener,const char *enm[],const char *unit)
+int get_ebin_space(t_ebin *eb, int nener, const char *enm[], const char *unit)
{
- int index;
- int i,f;
+ int index;
+ int i, f;
const char *u;
- index = eb->nener;
+ index = eb->nener;
eb->nener += nener;
- srenew(eb->e,eb->nener);
- srenew(eb->e_sim,eb->nener);
- srenew(eb->enm,eb->nener);
- for(i=index; (i<eb->nener); i++)
+ srenew(eb->e, eb->nener);
+ srenew(eb->e_sim, eb->nener);
+ srenew(eb->enm, eb->nener);
+ for (i = index; (i < eb->nener); i++)
{
eb->e[i].e = 0;
eb->e[i].eav = 0;
eb->e_sim[i].e = 0;
eb->e_sim[i].eav = 0;
eb->e_sim[i].esum = 0;
- eb->enm[i].name = strdup(enm[i-index]);
+ eb->enm[i].name = gmx_strdup(enm[i-index]);
if (unit != NULL)
{
- eb->enm[i].unit = strdup(unit);
+ eb->enm[i].unit = gmx_strdup(unit);
}
else
{
* entries would be removed from the ifunc array.
*/
u = unit_energy;
- for(f=0; f<F_NRE; f++)
+ for (f = 0; f < F_NRE; f++)
{
if (strcmp(eb->enm[i].name,
interaction_function[f].longname) == 0)
{
/* Only the terms in this list are not energies */
- switch (f) {
- case F_DISRESVIOL: u = unit_length; break;
- case F_ORIRESDEV: u = "obs"; break;
- case F_TEMP: u = unit_temp_K; break;
- case F_VTEMP: u = unit_temp_K; break;
- case F_PDISPCORR:
- case F_PRES: u = unit_pres_bar; break;
+ switch (f)
+ {
+ case F_DISRESVIOL: u = unit_length; break;
+ case F_ORIRESDEV: u = "obs"; break;
+ case F_TEMP: u = unit_temp_K; break;
+ case F_PDISPCORR:
+ case F_PRES: u = unit_pres_bar; break;
}
}
}
- eb->enm[i].unit = strdup(u);
+ eb->enm[i].unit = gmx_strdup(u);
}
}
-
+
return index;
}
-void add_ebin(t_ebin *eb,int index,int nener,real ener[],gmx_bool bSum)
+void add_ebin(t_ebin *eb, int index, int nener, real ener[], gmx_bool bSum)
{
- int i,m;
- double e,sum,sigma,invmm,diff;
- t_energy *eg,*egs;
-
+ int i, m;
+ double e, sum, sigma, invmm, diff;
+ t_energy *eg, *egs;
+
if ((index+nener > eb->nener) || (index < 0))
{
- gmx_fatal(FARGS,"%s-%d: Energies out of range: index=%d nener=%d maxener=%d",
- __FILE__,__LINE__,index,nener,eb->nener);
+ gmx_fatal(FARGS, "%s-%d: Energies out of range: index=%d nener=%d maxener=%d",
+ __FILE__, __LINE__, index, nener, eb->nener);
}
-
+
eg = &(eb->e[index]);
-
- for(i=0; (i<nener); i++)
+
+ for (i = 0; (i < nener); i++)
{
eg[i].e = ener[i];
}
-
+
if (bSum)
{
egs = &(eb->e_sim[index]);
-
+
m = eb->nsum;
-
+
if (m == 0)
{
- for(i=0; (i<nener); i++)
+ for (i = 0; (i < nener); i++)
{
eg[i].eav = 0;
eg[i].esum = ener[i];
else
{
invmm = (1.0/(double)m)/((double)m+1.0);
-
- for(i=0; (i<nener); i++)
+
+ for (i = 0; (i < nener); i++)
{
/* Value for this component */
e = ener[i];
-
+
/* first update sigma, then sum */
diff = eg[i].esum - m*e;
eg[i].eav += diff*diff*invmm;
}
}
-void ebin_increase_count(t_ebin *eb,gmx_bool bSum)
+void ebin_increase_count(t_ebin *eb, gmx_bool bSum)
{
eb->nsteps++;
eb->nsteps_sim++;
/* The actual sums are cleared when the next frame is stored */
}
-void pr_ebin(FILE *fp,t_ebin *eb,int index,int nener,int nperline,
- int prmode,gmx_bool bPrHead)
+void pr_ebin(FILE *fp, t_ebin *eb, int index, int nener, int nperline,
+ int prmode, gmx_bool bPrHead)
{
- int i,j,i0;
- real ee=0;
+ int i, j, i0;
+ real ee = 0;
int rc;
char buf[30];
if (index < 0)
{
- gmx_fatal(FARGS,"Invalid index in pr_ebin: %d",index);
+ gmx_fatal(FARGS, "Invalid index in pr_ebin: %d", index);
}
if (nener == -1)
{
{
nener = index + nener;
}
- for(i=index; (i<nener) && rc>=0; )
+ for (i = index; (i < nener) && rc >= 0; )
{
if (bPrHead)
{
- i0=i;
- for(j=0; (j<nperline) && (i<nener) && rc>=0; j++,i++)
+ i0 = i;
+ for (j = 0; (j < nperline) && (i < nener) && rc >= 0; j++, i++)
{
- if (strncmp(eb->enm[i].name,"Pres",4) == 0)
+ if (strncmp(eb->enm[i].name, "Pres", 4) == 0)
{
/* Print the pressure unit to avoid confusion */
- sprintf(buf,"%s (%s)",eb->enm[i].name,unit_pres_bar);
- rc = fprintf(fp,"%15s",buf);
+ sprintf(buf, "%s (%s)", eb->enm[i].name, unit_pres_bar);
+ rc = fprintf(fp, "%15s", buf);
}
else
{
- rc = fprintf(fp,"%15s",eb->enm[i].name);
+ rc = fprintf(fp, "%15s", eb->enm[i].name);
}
}
if (rc >= 0)
{
- rc = fprintf(fp,"\n");
+ rc = fprintf(fp, "\n");
}
- i=i0;
+ i = i0;
}
- for(j=0; (j<nperline) && (i<nener) && rc>=0; j++,i++)
+ for (j = 0; (j < nperline) && (i < nener) && rc >= 0; j++, i++)
{
- switch (prmode) {
+ switch (prmode)
+ {
case eprNORMAL: ee = eb->e[i].e; break;
case eprAVER: ee = eb->e_sim[i].esum/eb->nsum_sim; break;
- default: gmx_fatal(FARGS,"Invalid print mode %d in pr_ebin",
+ default: gmx_fatal(FARGS, "Invalid print mode %d in pr_ebin",
prmode);
}
- rc = fprintf(fp," %12.5e",ee);
+ rc = fprintf(fp, " %12.5e", ee);
}
if (rc >= 0)
{
- rc = fprintf(fp,"\n");
+ rc = fprintf(fp, "\n");
}
}
if (rc < 0)
- {
- gmx_fatal(FARGS,"Cannot write to logfile; maybe you are out of disk space?");
+ {
+ gmx_fatal(FARGS, "Cannot write to logfile; maybe you are out of disk space?");
}
}
#ifdef DEBUGEBIN
-int main(int argc,char *argv[])
+int main(int argc, char *argv[])
{
#define NE 12
#define NT 7
#define NS 5
- t_ebin *eb;
- int i;
- char buf[25];
- char *ce[NE],*ct[NT],*cs[NS];
- real e[NE],t[NT],s[NS];
- int ie,it,is;
-
- eb=mk_ebin();
- for(i=0; (i<NE); i++) {
- e[i]=i;
- sprintf(buf,"e%d",i);
- ce[i]=strdup(buf);
- }
- ie=get_ebin_space(eb,NE,ce);
- add_ebin(eb,ie,NE,e,0);
- for(i=0; (i<NS); i++) {
- s[i]=i;
- sprintf(buf,"s%d",i);
- cs[i]=strdup(buf);
- }
- is=get_ebin_space(eb,NS,cs);
- add_ebin(eb,is,NS,s,0);
- for(i=0; (i<NT); i++) {
- t[i]=i;
- sprintf(buf,"t%d",i);
- ct[i]=strdup(buf);
- }
- it=get_ebin_space(eb,NT,ct);
- add_ebin(eb,it,NT,t,0);
-
- printf("Normal:\n");
- pr_ebin(stdout,eb,0,-1,5,eprNORMAL,1);
+ t_ebin *eb;
+ int i;
+ char buf[25];
+ char *ce[NE], *ct[NT], *cs[NS];
+ real e[NE], t[NT], s[NS];
+ int ie, it, is;
+
+ eb = mk_ebin();
+ for (i = 0; (i < NE); i++)
+ {
+ e[i] = i;
+ sprintf(buf, "e%d", i);
+ ce[i] = gmx_strdup(buf);
+ }
+ ie = get_ebin_space(eb, NE, ce);
+ add_ebin(eb, ie, NE, e, 0);
+ for (i = 0; (i < NS); i++)
+ {
+ s[i] = i;
+ sprintf(buf, "s%d", i);
+ cs[i] = gmx_strdup(buf);
+ }
+ is = get_ebin_space(eb, NS, cs);
+ add_ebin(eb, is, NS, s, 0);
+ for (i = 0; (i < NT); i++)
+ {
+ t[i] = i;
+ sprintf(buf, "t%d", i);
+ ct[i] = gmx_strdup(buf);
+ }
+ it = get_ebin_space(eb, NT, ct);
+ add_ebin(eb, it, NT, t, 0);
+
+ printf("Normal:\n");
+ pr_ebin(stdout, eb, 0, -1, 5, eprNORMAL, 1);
- printf("Average:\n");
- pr_ebin(stdout,eb,ie,NE,5,eprAVER,1);
- pr_ebin(stdout,eb,is,NS,3,eprAVER,1);
- pr_ebin(stdout,eb,it,NT,4,eprAVER,1);
+ printf("Average:\n");
+ pr_ebin(stdout, eb, ie, NE, 5, eprAVER, 1);
+ pr_ebin(stdout, eb, is, NS, 3, eprAVER, 1);
+ pr_ebin(stdout, eb, it, NT, 4, eprAVER, 1);
}
#endif
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