Improved version for builds from modified trees.
[gromacs/qmmm-gamess-us.git] / src / mdlib / rf_util.c
blobcc4194129483f5ee3587a8501fc3f2ae93b7f2ef
1 /*
2 *
3 * This source code is part of
4 *
5 * G R O M A C S
6 *
7 * GROningen MAchine for Chemical Simulations
8 *
9 * VERSION 3.2.0
10 * Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
11 * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
12 * Copyright (c) 2001-2004, The GROMACS development team,
13 * check out http://www.gromacs.org for more information.
15 * This program is free software; you can redistribute it and/or
16 * modify it under the terms of the GNU General Public License
17 * as published by the Free Software Foundation; either version 2
18 * of the License, or (at your option) any later version.
20 * If you want to redistribute modifications, please consider that
21 * scientific software is very special. Version control is crucial -
22 * bugs must be traceable. We will be happy to consider code for
23 * inclusion in the official distribution, but derived work must not
24 * be called official GROMACS. Details are found in the README & COPYING
25 * files - if they are missing, get the official version at www.gromacs.org.
27 * To help us fund GROMACS development, we humbly ask that you cite
28 * the papers on the package - you can find them in the top README file.
30 * For more info, check our website at http://www.gromacs.org
32 * And Hey:
33 * GROwing Monsters And Cloning Shrimps
35 #ifdef HAVE_CONFIG_H
36 #include <config.h>
37 #endif
39 #include "sysstuff.h"
40 #include "typedefs.h"
41 #include "force.h"
42 #include "names.h"
43 #include "vec.h"
44 #include "physics.h"
45 #include "copyrite.h"
46 #include "pbc.h"
48 real RF_excl_correction(FILE *log,
49 const t_forcerec *fr,t_graph *g,
50 const t_mdatoms *mdatoms,const t_blocka *excl,
51 rvec x[],rvec f[],rvec *fshift,const t_pbc *pbc,
52 real lambda,real *dvdlambda)
54 /* Calculate the reaction-field energy correction for this node:
55 * epsfac q_i q_j (k_rf r_ij^2 - c_rf)
56 * and force correction for all excluded pairs, including self pairs.
58 int top,i,j,j1,j2,k,ki;
59 double q2sumA,q2sumB,ener;
60 const real *chargeA,*chargeB;
61 real ek,ec,L1,qiA,qiB,qqA,qqB,qqL,v;
62 rvec dx,df;
63 atom_id *AA;
64 ivec dt;
65 int start = mdatoms->start;
66 int end = mdatoms->homenr+start;
67 int niat;
68 bool bMolPBC = fr->bMolPBC;
70 if (fr->n_tpi)
71 /* For test particle insertion we only correct for the test molecule */
72 start = mdatoms->nr - fr->n_tpi;
74 ek = fr->epsfac*fr->k_rf;
75 ec = fr->epsfac*fr->c_rf;
76 chargeA = mdatoms->chargeA;
77 chargeB = mdatoms->chargeB;
78 AA = excl->a;
79 ki = CENTRAL;
81 if (fr->bDomDec)
82 niat = excl->nr;
83 else
84 niat = end;
86 q2sumA = 0;
87 q2sumB = 0;
88 ener = 0;
89 if (mdatoms->nChargePerturbed == 0) {
90 for(i=start; i<niat; i++) {
91 qiA = chargeA[i];
92 if (i < end)
93 q2sumA += qiA*qiA;
94 /* Do the exclusions */
95 j1 = excl->index[i];
96 j2 = excl->index[i+1];
97 for(j=j1; j<j2; j++) {
98 k = AA[j];
99 if (k > i) {
100 qqA = qiA*chargeA[k];
101 if (qqA != 0) {
102 if (g) {
103 rvec_sub(x[i],x[k],dx);
104 ivec_sub(SHIFT_IVEC(g,i),SHIFT_IVEC(g,k),dt);
105 ki=IVEC2IS(dt);
106 } else if (bMolPBC) {
107 ki = pbc_dx_aiuc(pbc,x[i],x[k],dx);
108 } else
109 rvec_sub(x[i],x[k],dx);
110 ener += qqA*(ek*norm2(dx) - ec);
111 svmul(-2*qqA*ek,dx,df);
112 rvec_inc(f[i],df);
113 rvec_dec(f[k],df);
114 rvec_inc(fshift[ki],df);
115 rvec_dec(fshift[CENTRAL],df);
120 ener += -0.5*ec*q2sumA;
121 } else {
122 L1 = 1.0 - lambda;
123 for(i=start; i<niat; i++) {
124 qiA = chargeA[i];
125 qiB = chargeB[i];
126 if (i < end) {
127 q2sumA += qiA*qiA;
128 q2sumB += qiB*qiB;
130 /* Do the exclusions */
131 j1 = excl->index[i];
132 j2 = excl->index[i+1];
133 for(j=j1; j<j2; j++) {
134 k = AA[j];
135 if (k > i) {
136 qqA = qiA*chargeA[k];
137 qqB = qiB*chargeB[k];
138 if (qqA != 0 || qqB != 0) {
139 qqL = L1*qqA + lambda*qqB;
140 if (g) {
141 rvec_sub(x[i],x[k],dx);
142 ivec_sub(SHIFT_IVEC(g,i),SHIFT_IVEC(g,k),dt);
143 ki=IVEC2IS(dt);
144 } else if (bMolPBC) {
145 ki = pbc_dx_aiuc(pbc,x[i],x[k],dx);
146 } else
147 rvec_sub(x[i],x[k],dx);
148 v = ek*norm2(dx) - ec;
149 ener += qqL*v;
150 svmul(-2*qqL*ek,dx,df);
151 rvec_inc(f[i],df);
152 rvec_dec(f[k],df);
153 rvec_inc(fshift[ki],df);
154 rvec_dec(fshift[CENTRAL],df);
155 *dvdlambda += (qqB - qqA)*v;
160 ener += -0.5*ec*(L1*q2sumA + lambda*q2sumB);
161 *dvdlambda += -0.5*ec*(q2sumB - q2sumA);
164 if (debug)
165 fprintf(debug,"RF exclusion energy: %g\n",ener);
167 return ener;
170 void calc_rffac(FILE *fplog,int eel,real eps_r,real eps_rf,real Rc,real Temp,
171 real zsq,matrix box,
172 real *kappa,real *krf,real *crf)
174 /* Compute constants for Generalized reaction field */
175 real k1,k2,I,vol,rmin;
177 if (EEL_RF(eel)) {
178 vol = det(box);
179 if (eel == eelGRF) {
180 /* Consistency check */
181 if (Temp <= 0.0)
182 gmx_fatal(FARGS,"Temperature is %f while using"
183 " Generalized Reaction Field\n",Temp);
184 /* Ionic strength (only needed for eelGRF */
185 I = 0.5*zsq/vol;
186 *kappa = sqrt(2*I/(EPSILON0*eps_rf*BOLTZ*Temp));
188 else {
189 I = 0;
190 *kappa = 0;
193 /* eps == 0 signals infinite dielectric */
194 if (eps_rf == 0) {
195 *krf = 1/(2*Rc*Rc*Rc);
196 } else {
197 k1 = 1 + *kappa*Rc;
198 k2 = eps_rf*sqr((real)(*kappa*Rc));
200 *krf = ((eps_rf - eps_r)*k1 + 0.5*k2)/((2*eps_rf + eps_r)*k1 + k2)/(Rc*Rc*Rc);
202 *crf = 1/Rc + *krf*Rc*Rc;
203 rmin = pow(*krf*2.0,-1.0/3.0);
205 if (fplog) {
206 if (eel == eelGRF) {
207 please_cite(fplog,"Tironi95a");
208 fprintf(fplog,"%s:\n"
209 "epsRF = %10g, I = %10g, volume = %10g, kappa = %10g\n"
210 "rc = %10g, krf = %10g, crf = %10g, epsfac = %10g\n",
211 eel_names[eel],eps_rf,I,vol,*kappa,Rc,*krf,*crf,
212 ONE_4PI_EPS0/eps_r);
213 } else {
214 fprintf(fplog,"%s:\n"
215 "epsRF = %g, rc = %g, krf = %g, crf = %g, epsfac = %g\n",
216 eel_names[eel],eps_rf,Rc,*krf,*crf,ONE_4PI_EPS0/eps_r);
218 fprintf(fplog,
219 "The electrostatics potential has its minimum at r = %g\n",
220 rmin);
225 void init_generalized_rf(FILE *fplog,
226 const gmx_mtop_t *mtop,const t_inputrec *ir,
227 t_forcerec *fr)
229 int mb,i,j;
230 real q,zsq,nrdf,T;
231 const gmx_moltype_t *molt;
232 const t_block *cgs;
234 if (ir->efep != efepNO && fplog) {
235 fprintf(fplog,"\nWARNING: the generalized reaction field constants are determined from topology A only\n\n");
237 zsq = 0.0;
238 for(mb=0; mb<mtop->nmolblock; mb++) {
239 molt = &mtop->moltype[mtop->molblock[mb].type];
240 cgs = &molt->cgs;
241 for(i=0; (i<cgs->nr); i++) {
242 q = 0;
243 for(j=cgs->index[i]; (j<cgs->index[i+1]); j++) {
244 q += molt->atoms.atom[j].q;
246 zsq += mtop->molblock[mb].nmol*q*q;
248 fr->zsquare = zsq;
251 T = 0.0;
252 nrdf = 0.0;
253 for(i=0; (i<ir->opts.ngtc); i++) {
254 nrdf += ir->opts.nrdf[i];
255 T += (ir->opts.nrdf[i] * ir->opts.ref_t[i]);
257 if (nrdf == 0) {
258 gmx_fatal(FARGS,"No degrees of freedom!");
260 fr->temp = T/nrdf;