/*
- *
- * 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.
+ * This file is part of the GROMACS molecular simulation package.
+ *
* 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.
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- * as published by the Free Software Foundation; either version 2
+ * Copyright (c) 2001-2004, The GROMACS development team.
+ * Copyright (c) 2013,2014, 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.
+ *
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
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* of the License, or (at your option) any later version.
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*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
-#include "sysstuff.h"
-#include "typedefs.h"
-#include "force.h"
-#include "names.h"
-#include "vec.h"
-#include "physics.h"
-#include "copyrite.h"
-#include "pbc.h"
+#include "gromacs/legacyheaders/copyrite.h"
+#include "gromacs/legacyheaders/force.h"
+#include "gromacs/legacyheaders/names.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/math/units.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/pbcutil/ishift.h"
+#include "gromacs/pbcutil/mshift.h"
+#include "gromacs/pbcutil/pbc.h"
-real RF_excl_correction(FILE *log,
- const t_forcerec *fr,t_graph *g,
- const t_mdatoms *mdatoms,const t_blocka *excl,
- rvec x[],rvec f[],rvec *fshift,const t_pbc *pbc,
- real lambda,real *dvdlambda)
+real RF_excl_correction(const t_forcerec *fr, t_graph *g,
+ const t_mdatoms *mdatoms, const t_blocka *excl,
+ rvec x[], rvec f[], rvec *fshift, const t_pbc *pbc,
+ real lambda, real *dvdlambda)
{
- /* Calculate the reaction-field energy correction for this node:
- * epsfac q_i q_j (k_rf r_ij^2 - c_rf)
- * and force correction for all excluded pairs, including self pairs.
- */
- int top,i,j,j1,j2,k,ki;
- double q2sumA,q2sumB,ener;
- const real *chargeA,*chargeB;
- real ek,ec,L1,qiA,qiB,qqA,qqB,qqL,v;
- rvec dx,df;
- atom_id *AA;
- ivec dt;
- int start = mdatoms->start;
- int end = mdatoms->homenr+start;
- int niat;
- gmx_bool bMolPBC = fr->bMolPBC;
-
- if (fr->n_tpi)
- /* For test particle insertion we only correct for the test molecule */
- start = mdatoms->nr - fr->n_tpi;
+ /* Calculate the reaction-field energy correction for this node:
+ * epsfac q_i q_j (k_rf r_ij^2 - c_rf)
+ * and force correction for all excluded pairs, including self pairs.
+ */
+ int top, i, j, j1, j2, k, ki;
+ double q2sumA, q2sumB, ener;
+ const real *chargeA, *chargeB;
+ real ek, ec, L1, qiA, qiB, qqA, qqB, qqL, v;
+ rvec dx, df;
+ atom_id *AA;
+ ivec dt;
+ int start = 0;
+ int end = mdatoms->homenr;
+ int niat;
+ gmx_bool bMolPBC = fr->bMolPBC;
- ek = fr->epsfac*fr->k_rf;
- ec = fr->epsfac*fr->c_rf;
- chargeA = mdatoms->chargeA;
- chargeB = mdatoms->chargeB;
- AA = excl->a;
- ki = CENTRAL;
+ if (fr->n_tpi)
+ {
+ /* For test particle insertion we only correct for the test molecule */
+ start = mdatoms->nr - fr->n_tpi;
+ }
- if (fr->bDomDec)
- niat = excl->nr;
- else
- niat = end;
+ ek = fr->epsfac*fr->k_rf;
+ ec = fr->epsfac*fr->c_rf;
+ chargeA = mdatoms->chargeA;
+ chargeB = mdatoms->chargeB;
+ AA = excl->a;
+ ki = CENTRAL;
- q2sumA = 0;
- q2sumB = 0;
- ener = 0;
- if (mdatoms->nChargePerturbed == 0) {
- for(i=start; i<niat; i++) {
- qiA = chargeA[i];
- if (i < end)
- q2sumA += qiA*qiA;
- /* Do the exclusions */
- j1 = excl->index[i];
- j2 = excl->index[i+1];
- for(j=j1; j<j2; j++) {
- k = AA[j];
- if (k > i) {
- qqA = qiA*chargeA[k];
- if (qqA != 0) {
- if (g) {
- rvec_sub(x[i],x[k],dx);
- ivec_sub(SHIFT_IVEC(g,i),SHIFT_IVEC(g,k),dt);
- ki=IVEC2IS(dt);
- } else if (bMolPBC) {
- ki = pbc_dx_aiuc(pbc,x[i],x[k],dx);
- } else
- rvec_sub(x[i],x[k],dx);
- ener += qqA*(ek*norm2(dx) - ec);
- svmul(-2*qqA*ek,dx,df);
- rvec_inc(f[i],df);
- rvec_dec(f[k],df);
- rvec_inc(fshift[ki],df);
- rvec_dec(fshift[CENTRAL],df);
- }
- }
- }
+ if (fr->bDomDec)
+ {
+ niat = excl->nr;
}
- ener += -0.5*ec*q2sumA;
- } else {
- L1 = 1.0 - lambda;
- for(i=start; i<niat; i++) {
- qiA = chargeA[i];
- qiB = chargeB[i];
- if (i < end) {
- q2sumA += qiA*qiA;
- q2sumB += qiB*qiB;
- }
- /* Do the exclusions */
- j1 = excl->index[i];
- j2 = excl->index[i+1];
- for(j=j1; j<j2; j++) {
- k = AA[j];
- if (k > i) {
- qqA = qiA*chargeA[k];
- qqB = qiB*chargeB[k];
- if (qqA != 0 || qqB != 0) {
- qqL = L1*qqA + lambda*qqB;
- if (g) {
- rvec_sub(x[i],x[k],dx);
- ivec_sub(SHIFT_IVEC(g,i),SHIFT_IVEC(g,k),dt);
- ki=IVEC2IS(dt);
- } else if (bMolPBC) {
- ki = pbc_dx_aiuc(pbc,x[i],x[k],dx);
- } else
- rvec_sub(x[i],x[k],dx);
- v = ek*norm2(dx) - ec;
- ener += qqL*v;
- svmul(-2*qqL*ek,dx,df);
- rvec_inc(f[i],df);
- rvec_dec(f[k],df);
- rvec_inc(fshift[ki],df);
- rvec_dec(fshift[CENTRAL],df);
- *dvdlambda += (qqB - qqA)*v;
- }
- }
- }
+ else
+ {
+ niat = end;
}
- ener += -0.5*ec*(L1*q2sumA + lambda*q2sumB);
- *dvdlambda += -0.5*ec*(q2sumB - q2sumA);
- }
-
- if (debug)
- fprintf(debug,"RF exclusion energy: %g\n",ener);
-
- return ener;
-}
-void calc_rffac(FILE *fplog,int eel,real eps_r,real eps_rf,real Rc,real Temp,
- real zsq,matrix box,
- real *kappa,real *krf,real *crf)
-{
- /* Compute constants for Generalized reaction field */
- real k1,k2,I,vol,rmin;
-
- if (EEL_RF(eel)) {
- vol = det(box);
- if (eel == eelGRF) {
- /* Consistency check */
- if (Temp <= 0.0)
- gmx_fatal(FARGS,"Temperature is %f while using"
- " Generalized Reaction Field\n",Temp);
- /* Ionic strength (only needed for eelGRF */
- I = 0.5*zsq/vol;
- *kappa = sqrt(2*I/(EPSILON0*eps_rf*BOLTZ*Temp));
+ q2sumA = 0;
+ q2sumB = 0;
+ ener = 0;
+ if (mdatoms->nChargePerturbed == 0)
+ {
+ for (i = start; i < niat; i++)
+ {
+ qiA = chargeA[i];
+ if (i < end)
+ {
+ q2sumA += qiA*qiA;
+ }
+ /* Do the exclusions */
+ j1 = excl->index[i];
+ j2 = excl->index[i+1];
+ for (j = j1; j < j2; j++)
+ {
+ k = AA[j];
+ if (k > i)
+ {
+ qqA = qiA*chargeA[k];
+ if (qqA != 0)
+ {
+ if (g)
+ {
+ rvec_sub(x[i], x[k], dx);
+ ivec_sub(SHIFT_IVEC(g, i), SHIFT_IVEC(g, k), dt);
+ ki = IVEC2IS(dt);
+ }
+ else if (bMolPBC)
+ {
+ ki = pbc_dx_aiuc(pbc, x[i], x[k], dx);
+ }
+ else
+ {
+ rvec_sub(x[i], x[k], dx);
+ }
+ ener += qqA*(ek*norm2(dx) - ec);
+ svmul(-2*qqA*ek, dx, df);
+ rvec_inc(f[i], df);
+ rvec_dec(f[k], df);
+ rvec_inc(fshift[ki], df);
+ rvec_dec(fshift[CENTRAL], df);
+ }
+ }
+ }
+ }
+ ener += -0.5*ec*q2sumA;
}
- else {
- I = 0;
- *kappa = 0;
+ else
+ {
+ L1 = 1.0 - lambda;
+ for (i = start; i < niat; i++)
+ {
+ qiA = chargeA[i];
+ qiB = chargeB[i];
+ if (i < end)
+ {
+ q2sumA += qiA*qiA;
+ q2sumB += qiB*qiB;
+ }
+ /* Do the exclusions */
+ j1 = excl->index[i];
+ j2 = excl->index[i+1];
+ for (j = j1; j < j2; j++)
+ {
+ k = AA[j];
+ if (k > i)
+ {
+ qqA = qiA*chargeA[k];
+ qqB = qiB*chargeB[k];
+ if (qqA != 0 || qqB != 0)
+ {
+ qqL = L1*qqA + lambda*qqB;
+ if (g)
+ {
+ rvec_sub(x[i], x[k], dx);
+ ivec_sub(SHIFT_IVEC(g, i), SHIFT_IVEC(g, k), dt);
+ ki = IVEC2IS(dt);
+ }
+ else if (bMolPBC)
+ {
+ ki = pbc_dx_aiuc(pbc, x[i], x[k], dx);
+ }
+ else
+ {
+ rvec_sub(x[i], x[k], dx);
+ }
+ v = ek*norm2(dx) - ec;
+ ener += qqL*v;
+ svmul(-2*qqL*ek, dx, df);
+ rvec_inc(f[i], df);
+ rvec_dec(f[k], df);
+ rvec_inc(fshift[ki], df);
+ rvec_dec(fshift[CENTRAL], df);
+ *dvdlambda += (qqB - qqA)*v;
+ }
+ }
+ }
+ }
+ ener += -0.5*ec*(L1*q2sumA + lambda*q2sumB);
+ *dvdlambda += -0.5*ec*(q2sumB - q2sumA);
}
- /* eps == 0 signals infinite dielectric */
- if (eps_rf == 0) {
- *krf = 1/(2*Rc*Rc*Rc);
- } else {
- k1 = 1 + *kappa*Rc;
- k2 = eps_rf*sqr((real)(*kappa*Rc));
-
- *krf = ((eps_rf - eps_r)*k1 + 0.5*k2)/((2*eps_rf + eps_r)*k1 + k2)/(Rc*Rc*Rc);
+ if (debug)
+ {
+ fprintf(debug, "RF exclusion energy: %g\n", ener);
}
- *crf = 1/Rc + *krf*Rc*Rc;
- rmin = pow(*krf*2.0,-1.0/3.0);
-
- if (fplog) {
- if (eel == eelGRF) {
- please_cite(fplog,"Tironi95a");
- fprintf(fplog,"%s:\n"
- "epsRF = %10g, I = %10g, volume = %10g, kappa = %10g\n"
- "rc = %10g, krf = %10g, crf = %10g, epsfac = %10g\n",
- eel_names[eel],eps_rf,I,vol,*kappa,Rc,*krf,*crf,
- ONE_4PI_EPS0/eps_r);
- } else {
- fprintf(fplog,"%s:\n"
- "epsRF = %g, rc = %g, krf = %g, crf = %g, epsfac = %g\n",
- eel_names[eel],eps_rf,Rc,*krf,*crf,ONE_4PI_EPS0/eps_r);
- }
- fprintf(fplog,
- "The electrostatics potential has its minimum at r = %g\n",
- rmin);
+
+ return ener;
+}
+
+void calc_rffac(FILE *fplog, int eel, real eps_r, real eps_rf, real Rc, real Temp,
+ real zsq, matrix box,
+ real *kappa, real *krf, real *crf)
+{
+ /* Compute constants for Generalized reaction field */
+ real k1, k2, I, vol, rmin;
+
+ if (EEL_RF(eel))
+ {
+ vol = det(box);
+ if (eel == eelGRF)
+ {
+ /* Consistency check */
+ if (Temp <= 0.0)
+ {
+ gmx_fatal(FARGS, "Temperature is %f while using"
+ " Generalized Reaction Field\n", Temp);
+ }
+ /* Ionic strength (only needed for eelGRF */
+ I = 0.5*zsq/vol;
+ *kappa = sqrt(2*I/(EPSILON0*eps_rf*BOLTZ*Temp));
+ }
+ else
+ {
+ I = 0;
+ *kappa = 0;
+ }
+
+ /* eps == 0 signals infinite dielectric */
+ if (eps_rf == 0)
+ {
+ *krf = 1/(2*Rc*Rc*Rc);
+ }
+ else
+ {
+ k1 = 1 + *kappa*Rc;
+ k2 = eps_rf*sqr((real)(*kappa*Rc));
+
+ *krf = ((eps_rf - eps_r)*k1 + 0.5*k2)/((2*eps_rf + eps_r)*k1 + k2)/(Rc*Rc*Rc);
+ }
+ *crf = 1/Rc + *krf*Rc*Rc;
+ rmin = pow(*krf*2.0, -1.0/3.0);
+
+ if (fplog)
+ {
+ if (eel == eelGRF)
+ {
+ please_cite(fplog, "Tironi95a");
+ fprintf(fplog, "%s:\n"
+ "epsRF = %10g, I = %10g, volume = %10g, kappa = %10g\n"
+ "rc = %10g, krf = %10g, crf = %10g, epsfac = %10g\n",
+ eel_names[eel], eps_rf, I, vol, *kappa, Rc, *krf, *crf,
+ ONE_4PI_EPS0/eps_r);
+ }
+ else
+ {
+ fprintf(fplog, "%s:\n"
+ "epsRF = %g, rc = %g, krf = %g, crf = %g, epsfac = %g\n",
+ eel_names[eel], eps_rf, Rc, *krf, *crf, ONE_4PI_EPS0/eps_r);
+ }
+ fprintf(fplog,
+ "The electrostatics potential has its minimum at r = %g\n",
+ rmin);
+ }
}
- }
}
void init_generalized_rf(FILE *fplog,
- const gmx_mtop_t *mtop,const t_inputrec *ir,
- t_forcerec *fr)
+ const gmx_mtop_t *mtop, const t_inputrec *ir,
+ t_forcerec *fr)
{
- int mb,i,j;
- real q,zsq,nrdf,T;
- const gmx_moltype_t *molt;
- const t_block *cgs;
+ int mb, i, j;
+ real q, zsq, nrdf, T;
+ const gmx_moltype_t *molt;
+ const t_block *cgs;
- if (ir->efep != efepNO && fplog) {
- fprintf(fplog,"\nWARNING: the generalized reaction field constants are determined from topology A only\n\n");
- }
- zsq = 0.0;
- for(mb=0; mb<mtop->nmolblock; mb++) {
- molt = &mtop->moltype[mtop->molblock[mb].type];
- cgs = &molt->cgs;
- for(i=0; (i<cgs->nr); i++) {
- q = 0;
- for(j=cgs->index[i]; (j<cgs->index[i+1]); j++) {
- q += molt->atoms.atom[j].q;
- }
- zsq += mtop->molblock[mb].nmol*q*q;
+ if (ir->efep != efepNO && fplog)
+ {
+ fprintf(fplog, "\nWARNING: the generalized reaction field constants are determined from topology A only\n\n");
+ }
+ zsq = 0.0;
+ for (mb = 0; mb < mtop->nmolblock; mb++)
+ {
+ molt = &mtop->moltype[mtop->molblock[mb].type];
+ cgs = &molt->cgs;
+ for (i = 0; (i < cgs->nr); i++)
+ {
+ q = 0;
+ for (j = cgs->index[i]; (j < cgs->index[i+1]); j++)
+ {
+ q += molt->atoms.atom[j].q;
+ }
+ zsq += mtop->molblock[mb].nmol*q*q;
+ }
+ fr->zsquare = zsq;
+ }
+
+ T = 0.0;
+ nrdf = 0.0;
+ for (i = 0; (i < ir->opts.ngtc); i++)
+ {
+ nrdf += ir->opts.nrdf[i];
+ T += (ir->opts.nrdf[i] * ir->opts.ref_t[i]);
+ }
+ if (nrdf == 0)
+ {
+ gmx_fatal(FARGS, "No degrees of freedom!");
}
- fr->zsquare = zsq;
- }
-
- T = 0.0;
- nrdf = 0.0;
- for(i=0; (i<ir->opts.ngtc); i++) {
- nrdf += ir->opts.nrdf[i];
- T += (ir->opts.nrdf[i] * ir->opts.ref_t[i]);
- }
- if (nrdf == 0) {
- gmx_fatal(FARGS,"No degrees of freedom!");
- }
- fr->temp = T/nrdf;
+ fr->temp = T/nrdf;
}
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff