/*
- *
+ *
* 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.
* 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:
* Gallium Rubidium Oxygen Manganese Argon Carbon Silicon
*/
#include "gpp_atomtype.h"
#include "maths.h"
-static int round_check(real r,int limit,int ftype,const char *name)
+static int round_check(real r, int limit, int ftype, const char *name)
{
- int i;
+ int i;
- if (r >= 0)
- i = (int)(r + 0.5);
- else
- i = (int)(r - 0.5);
+ if (r >= 0)
+ {
+ i = (int)(r + 0.5);
+ }
+ else
+ {
+ i = (int)(r - 0.5);
+ }
- if (r-i > 0.01 || r-i < -0.01)
- gmx_fatal(FARGS,"A non-integer value (%f) was supplied for '%s' in %s",
- r,name,interaction_function[ftype].longname);
+ if (r-i > 0.01 || r-i < -0.01)
+ {
+ gmx_fatal(FARGS, "A non-integer value (%f) was supplied for '%s' in %s",
+ r, name, interaction_function[ftype].longname);
+ }
- if (i < limit)
- gmx_fatal(FARGS,"Value of '%s' in %s is %d, which is smaller than the minimum of %d",
- name,interaction_function[ftype].longname,i,limit);
+ if (i < limit)
+ {
+ gmx_fatal(FARGS, "Value of '%s' in %s is %d, which is smaller than the minimum of %d",
+ name, interaction_function[ftype].longname, i, limit);
+ }
- return i;
+ return i;
}
-static void set_ljparams(int comb,double reppow,real v,real w,
- real *c6,real *c12)
+static void set_ljparams(int comb, double reppow, real v, real w,
+ real *c6, real *c12)
{
- if (comb == eCOMB_ARITHMETIC || comb == eCOMB_GEOM_SIG_EPS) {
- if (v >= 0) {
- *c6 = 4*w*pow(v,6.0);
- *c12 = 4*w*pow(v,reppow);
- } else {
- /* Interpret negative sigma as c6=0 and c12 with -sigma */
- *c6 = 0;
- *c12 = 4*w*pow(-v,reppow);
+ if (comb == eCOMB_ARITHMETIC || comb == eCOMB_GEOM_SIG_EPS)
+ {
+ if (v >= 0)
+ {
+ *c6 = 4*w*pow(v, 6.0);
+ *c12 = 4*w*pow(v, reppow);
+ }
+ else
+ {
+ /* Interpret negative sigma as c6=0 and c12 with -sigma */
+ *c6 = 0;
+ *c12 = 4*w*pow(-v, reppow);
+ }
+ }
+ else
+ {
+ *c6 = v;
+ *c12 = w;
}
- } else {
- *c6 = v;
- *c12 = w;
- }
}
/* A return value of 0 means parameters were assigned successfully,
* returning -1 means this is an all-zero interaction that should not be added.
*/
static int
-assign_param(t_functype ftype,t_iparams *newparam,
- real old[MAXFORCEPARAM],int comb,double reppow)
+assign_param(t_functype ftype, t_iparams *newparam,
+ real old[MAXFORCEPARAM], int comb, double reppow)
{
- int i,j;
- real tmp;
- gmx_bool all_param_zero=TRUE;
-
- /* Set to zero */
- for(j=0; (j<MAXFORCEPARAM); j++)
- {
- newparam->generic.buf[j]=0.0;
- /* If all parameters are zero we might not add some interaction types (selected below).
- * We cannot apply this to ALL interactions, since many have valid reasons for having
- * zero parameters (e.g. an index to a Cmap interaction, or LJ parameters), but
- * we use it for angles and torsions that are typically generated automatically.
- */
- all_param_zero = (all_param_zero==TRUE) && fabs(old[j])<GMX_REAL_MIN;
- }
-
- if(all_param_zero==TRUE)
- {
- if(IS_ANGLE(ftype) || IS_RESTRAINT_TYPE(ftype) || ftype==F_IDIHS ||
- ftype==F_PDIHS || ftype==F_PIDIHS || ftype==F_RBDIHS || ftype==F_FOURDIHS)
- {
- return -1;
- }
- }
-
- switch (ftype) {
- case F_G96ANGLES:
- /* Post processing of input data: store cosine iso angle itself */
- newparam->harmonic.rA =cos(old[0]*DEG2RAD);
- newparam->harmonic.krA=old[1];
- newparam->harmonic.rB =cos(old[2]*DEG2RAD);
- newparam->harmonic.krB=old[3];
- break;
- case F_G96BONDS:
- /* Post processing of input data: store square of length itself */
- newparam->harmonic.rA =sqr(old[0]);
- newparam->harmonic.krA=old[1];
- newparam->harmonic.rB =sqr(old[2]);
- newparam->harmonic.krB=old[3];
- break;
- case F_FENEBONDS:
- newparam->fene.bm=old[0];
- newparam->fene.kb=old[1];
- break;
- case F_RESTRBONDS:
- newparam->restraint.lowA = old[0];
- newparam->restraint.up1A = old[1];
- newparam->restraint.up2A = old[2];
- newparam->restraint.kA = old[3];
- newparam->restraint.lowB = old[4];
- newparam->restraint.up1B = old[5];
- newparam->restraint.up2B = old[6];
- newparam->restraint.kB = old[7];
- break;
- case F_TABBONDS:
- case F_TABBONDSNC:
- case F_TABANGLES:
- case F_TABDIHS:
- newparam->tab.table = round_check(old[0],0,ftype,"table index");
- newparam->tab.kA = old[1];
- newparam->tab.kB = old[3];
- break;
- case F_CROSS_BOND_BONDS:
- newparam->cross_bb.r1e=old[0];
- newparam->cross_bb.r2e=old[1];
- newparam->cross_bb.krr=old[2];
- break;
- case F_CROSS_BOND_ANGLES:
- newparam->cross_ba.r1e=old[0];
- newparam->cross_ba.r2e=old[1];
- newparam->cross_ba.r3e=old[2];
- newparam->cross_ba.krt=old[3];
- break;
- case F_UREY_BRADLEY:
- newparam->u_b.thetaA=old[0];
- newparam->u_b.kthetaA=old[1];
- newparam->u_b.r13A=old[2];
- newparam->u_b.kUBA=old[3];
- newparam->u_b.thetaB=old[4];
- newparam->u_b.kthetaB=old[5];
- newparam->u_b.r13B=old[6];
- newparam->u_b.kUBB=old[7];
- break;
- case F_QUARTIC_ANGLES:
- newparam->qangle.theta=old[0];
- for(i=0; i<5; i++)
- newparam->qangle.c[i]=old[i+1];
- break;
- case F_LINEAR_ANGLES:
- newparam->linangle.aA = old[0];
- newparam->linangle.klinA = old[1];
- newparam->linangle.aB = old[2];
- newparam->linangle.klinB = old[3];
- break;
- case F_BONDS:
- case F_ANGLES:
- case F_HARMONIC:
- case F_IDIHS:
- newparam->harmonic.rA =old[0];
- newparam->harmonic.krA=old[1];
- newparam->harmonic.rB =old[2];
- newparam->harmonic.krB=old[3];
- break;
- case F_MORSE:
- newparam->morse.b0A =old[0];
- newparam->morse.cbA =old[1];
- newparam->morse.betaA =old[2];
- newparam->morse.b0B =old[3];
- newparam->morse.cbB =old[4];
- newparam->morse.betaB =old[5];
- break;
- case F_CUBICBONDS:
- newparam->cubic.b0 =old[0];
- newparam->cubic.kb =old[1];
- newparam->cubic.kcub =old[2];
- break;
- case F_CONNBONDS:
- break;
- case F_POLARIZATION:
- newparam->polarize.alpha = old[0];
- break;
- case F_ANHARM_POL:
- newparam->anharm_polarize.alpha = old[0];
- newparam->anharm_polarize.drcut = old[1];
- newparam->anharm_polarize.khyp = old[2];
- break;
- case F_WATER_POL:
- newparam->wpol.al_x =old[0];
- newparam->wpol.al_y =old[1];
- newparam->wpol.al_z =old[2];
- newparam->wpol.rOH =old[3];
- newparam->wpol.rHH =old[4];
- newparam->wpol.rOD =old[5];
- break;
- case F_THOLE_POL:
- newparam->thole.a = old[0];
- newparam->thole.alpha1 = old[1];
- newparam->thole.alpha2 = old[2];
- if ((old[1] > 0) && (old[2] > 0))
- newparam->thole.rfac = old[0]*pow(old[1]*old[2],-1.0/6.0);
- else
- newparam->thole.rfac = 1;
- break;
- case F_BHAM:
- newparam->bham.a = old[0];
- newparam->bham.b = old[1];
- newparam->bham.c = old[2];
- break;
- case F_LJ14:
- set_ljparams(comb,reppow,old[0],old[1],&newparam->lj14.c6A,&newparam->lj14.c12A);
- set_ljparams(comb,reppow,old[2],old[3],&newparam->lj14.c6B,&newparam->lj14.c12B);
- break;
- case F_LJC14_Q:
- newparam->ljc14.fqq = old[0];
- newparam->ljc14.qi = old[1];
- newparam->ljc14.qj = old[2];
- set_ljparams(comb,reppow,old[3],old[4],&newparam->ljc14.c6,&newparam->ljc14.c12);
- break;
- case F_LJC_PAIRS_NB:
- newparam->ljcnb.qi = old[0];
- newparam->ljcnb.qj = old[1];
- set_ljparams(comb,reppow,old[2],old[3],&newparam->ljcnb.c6,&newparam->ljcnb.c12);
- break;
- case F_LJ:
- set_ljparams(comb,reppow,old[0],old[1],&newparam->lj.c6,&newparam->lj.c12);
- break;
- case F_PDIHS:
- case F_PIDIHS:
- case F_ANGRES:
- case F_ANGRESZ:
- newparam->pdihs.phiA = old[0];
- newparam->pdihs.cpA = old[1];
-
- /* Change 20100720: Amber occasionally uses negative multiplicities (mathematically OK),
- * so I have changed the lower limit to -99 /EL
- */
- newparam->pdihs.phiB = old[3];
- newparam->pdihs.cpB = old[4];
- /* If both force constants are zero there is no interaction. Return -1 to signal
- * this entry should NOT be added.
- */
- if( fabs(newparam->pdihs.cpA) < GMX_REAL_MIN && fabs(newparam->pdihs.cpB) < GMX_REAL_MIN )
- {
- return -1;
- }
-
- newparam->pdihs.mult = round_check(old[2],-99,ftype,"multiplicity");
-
- break;
- case F_POSRES:
- newparam->posres.fcA[XX] = old[0];
- newparam->posres.fcA[YY] = old[1];
- newparam->posres.fcA[ZZ] = old[2];
- newparam->posres.fcB[XX] = old[3];
- newparam->posres.fcB[YY] = old[4];
- newparam->posres.fcB[ZZ] = old[5];
- newparam->posres.pos0A[XX] = old[6];
- newparam->posres.pos0A[YY] = old[7];
- newparam->posres.pos0A[ZZ] = old[8];
- newparam->posres.pos0B[XX] = old[9];
- newparam->posres.pos0B[YY] = old[10];
- newparam->posres.pos0B[ZZ] = old[11];
- break;
- case F_FBPOSRES:
- newparam->fbposres.geom = round_check(old[0],0,ftype,"geometry");
- if ( ! (newparam->fbposres.geom > efbposresZERO && newparam->fbposres.geom < efbposresNR))
+ int i, j;
+ real tmp;
+ gmx_bool all_param_zero = TRUE;
+
+ /* Set to zero */
+ for (j = 0; (j < MAXFORCEPARAM); j++)
{
- gmx_fatal(FARGS,"Invalid geometry for flat-bottomed position restraint.\n"
- "Expected number between 1 and %d. Found %d\n", efbposresNR-1,
- newparam->fbposres.geom);
+ newparam->generic.buf[j] = 0.0;
+ /* If all parameters are zero we might not add some interaction types (selected below).
+ * We cannot apply this to ALL interactions, since many have valid reasons for having
+ * zero parameters (e.g. an index to a Cmap interaction, or LJ parameters), but
+ * we use it for angles and torsions that are typically generated automatically.
+ */
+ all_param_zero = (all_param_zero == TRUE) && fabs(old[j]) < GMX_REAL_MIN;
}
- newparam->fbposres.r = old[1];
- newparam->fbposres.k = old[2];
- newparam->fbposres.pos0[XX] = old[3];
- newparam->fbposres.pos0[YY] = old[4];
- newparam->fbposres.pos0[ZZ] = old[5];
- break;
- case F_DISRES:
- newparam->disres.label = round_check(old[0],0,ftype,"label");
- newparam->disres.type = round_check(old[1],1,ftype,"type'");
- newparam->disres.low = old[2];
- newparam->disres.up1 = old[3];
- newparam->disres.up2 = old[4];
- newparam->disres.kfac = old[5];
- break;
- case F_ORIRES:
- newparam->orires.ex = round_check(old[0],1,ftype,"experiment") - 1;
- newparam->orires.label = round_check(old[1],1,ftype,"label");
- newparam->orires.power = round_check(old[2],0,ftype,"power");
- newparam->orires.c = old[3];
- newparam->orires.obs = old[4];
- newparam->orires.kfac = old[5];
- break;
- case F_DIHRES:
- newparam->dihres.phiA = old[0];
- newparam->dihres.dphiA = old[1];
- newparam->dihres.kfacA = old[2];
- newparam->dihres.phiB = old[3];
- newparam->dihres.dphiB = old[4];
- newparam->dihres.kfacB = old[5];
- break;
- case F_RBDIHS:
- for (i=0; (i<NR_RBDIHS); i++) {
- newparam->rbdihs.rbcA[i]=old[i];
- newparam->rbdihs.rbcB[i]=old[NR_RBDIHS+i];
+
+ if (all_param_zero == TRUE)
+ {
+ if (IS_ANGLE(ftype) || IS_RESTRAINT_TYPE(ftype) || ftype == F_IDIHS ||
+ ftype == F_PDIHS || ftype == F_PIDIHS || ftype == F_RBDIHS || ftype == F_FOURDIHS)
+ {
+ return -1;
+ }
+ }
+
+ switch (ftype)
+ {
+ case F_G96ANGLES:
+ /* Post processing of input data: store cosine iso angle itself */
+ newparam->harmonic.rA = cos(old[0]*DEG2RAD);
+ newparam->harmonic.krA = old[1];
+ newparam->harmonic.rB = cos(old[2]*DEG2RAD);
+ newparam->harmonic.krB = old[3];
+ break;
+ case F_G96BONDS:
+ /* Post processing of input data: store square of length itself */
+ newparam->harmonic.rA = sqr(old[0]);
+ newparam->harmonic.krA = old[1];
+ newparam->harmonic.rB = sqr(old[2]);
+ newparam->harmonic.krB = old[3];
+ break;
+ case F_FENEBONDS:
+ newparam->fene.bm = old[0];
+ newparam->fene.kb = old[1];
+ break;
+ case F_RESTRBONDS:
+ newparam->restraint.lowA = old[0];
+ newparam->restraint.up1A = old[1];
+ newparam->restraint.up2A = old[2];
+ newparam->restraint.kA = old[3];
+ newparam->restraint.lowB = old[4];
+ newparam->restraint.up1B = old[5];
+ newparam->restraint.up2B = old[6];
+ newparam->restraint.kB = old[7];
+ break;
+ case F_TABBONDS:
+ case F_TABBONDSNC:
+ case F_TABANGLES:
+ case F_TABDIHS:
+ newparam->tab.table = round_check(old[0], 0, ftype, "table index");
+ newparam->tab.kA = old[1];
+ newparam->tab.kB = old[3];
+ break;
+ case F_CROSS_BOND_BONDS:
+ newparam->cross_bb.r1e = old[0];
+ newparam->cross_bb.r2e = old[1];
+ newparam->cross_bb.krr = old[2];
+ break;
+ case F_CROSS_BOND_ANGLES:
+ newparam->cross_ba.r1e = old[0];
+ newparam->cross_ba.r2e = old[1];
+ newparam->cross_ba.r3e = old[2];
+ newparam->cross_ba.krt = old[3];
+ break;
+ case F_UREY_BRADLEY:
+ newparam->u_b.thetaA = old[0];
+ newparam->u_b.kthetaA = old[1];
+ newparam->u_b.r13A = old[2];
+ newparam->u_b.kUBA = old[3];
+ newparam->u_b.thetaB = old[4];
+ newparam->u_b.kthetaB = old[5];
+ newparam->u_b.r13B = old[6];
+ newparam->u_b.kUBB = old[7];
+ break;
+ case F_QUARTIC_ANGLES:
+ newparam->qangle.theta = old[0];
+ for (i = 0; i < 5; i++)
+ {
+ newparam->qangle.c[i] = old[i+1];
+ }
+ break;
+ case F_LINEAR_ANGLES:
+ newparam->linangle.aA = old[0];
+ newparam->linangle.klinA = old[1];
+ newparam->linangle.aB = old[2];
+ newparam->linangle.klinB = old[3];
+ break;
+ case F_BONDS:
+ case F_ANGLES:
+ case F_HARMONIC:
+ case F_IDIHS:
+ newparam->harmonic.rA = old[0];
+ newparam->harmonic.krA = old[1];
+ newparam->harmonic.rB = old[2];
+ newparam->harmonic.krB = old[3];
+ break;
+ case F_MORSE:
+ newparam->morse.b0A = old[0];
+ newparam->morse.cbA = old[1];
+ newparam->morse.betaA = old[2];
+ newparam->morse.b0B = old[3];
+ newparam->morse.cbB = old[4];
+ newparam->morse.betaB = old[5];
+ break;
+ case F_CUBICBONDS:
+ newparam->cubic.b0 = old[0];
+ newparam->cubic.kb = old[1];
+ newparam->cubic.kcub = old[2];
+ break;
+ case F_CONNBONDS:
+ break;
+ case F_POLARIZATION:
+ newparam->polarize.alpha = old[0];
+ break;
+ case F_ANHARM_POL:
+ newparam->anharm_polarize.alpha = old[0];
+ newparam->anharm_polarize.drcut = old[1];
+ newparam->anharm_polarize.khyp = old[2];
+ break;
+ case F_WATER_POL:
+ newparam->wpol.al_x = old[0];
+ newparam->wpol.al_y = old[1];
+ newparam->wpol.al_z = old[2];
+ newparam->wpol.rOH = old[3];
+ newparam->wpol.rHH = old[4];
+ newparam->wpol.rOD = old[5];
+ break;
+ case F_THOLE_POL:
+ newparam->thole.a = old[0];
+ newparam->thole.alpha1 = old[1];
+ newparam->thole.alpha2 = old[2];
+ if ((old[1] > 0) && (old[2] > 0))
+ {
+ newparam->thole.rfac = old[0]*pow(old[1]*old[2], -1.0/6.0);
+ }
+ else
+ {
+ newparam->thole.rfac = 1;
+ }
+ break;
+ case F_BHAM:
+ newparam->bham.a = old[0];
+ newparam->bham.b = old[1];
+ newparam->bham.c = old[2];
+ break;
+ case F_LJ14:
+ set_ljparams(comb, reppow, old[0], old[1], &newparam->lj14.c6A, &newparam->lj14.c12A);
+ set_ljparams(comb, reppow, old[2], old[3], &newparam->lj14.c6B, &newparam->lj14.c12B);
+ break;
+ case F_LJC14_Q:
+ newparam->ljc14.fqq = old[0];
+ newparam->ljc14.qi = old[1];
+ newparam->ljc14.qj = old[2];
+ set_ljparams(comb, reppow, old[3], old[4], &newparam->ljc14.c6, &newparam->ljc14.c12);
+ break;
+ case F_LJC_PAIRS_NB:
+ newparam->ljcnb.qi = old[0];
+ newparam->ljcnb.qj = old[1];
+ set_ljparams(comb, reppow, old[2], old[3], &newparam->ljcnb.c6, &newparam->ljcnb.c12);
+ break;
+ case F_LJ:
+ set_ljparams(comb, reppow, old[0], old[1], &newparam->lj.c6, &newparam->lj.c12);
+ break;
+ case F_PDIHS:
+ case F_PIDIHS:
+ case F_ANGRES:
+ case F_ANGRESZ:
+ newparam->pdihs.phiA = old[0];
+ newparam->pdihs.cpA = old[1];
+
+ /* Change 20100720: Amber occasionally uses negative multiplicities (mathematically OK),
+ * so I have changed the lower limit to -99 /EL
+ */
+ newparam->pdihs.phiB = old[3];
+ newparam->pdihs.cpB = old[4];
+ /* If both force constants are zero there is no interaction. Return -1 to signal
+ * this entry should NOT be added.
+ */
+ if (fabs(newparam->pdihs.cpA) < GMX_REAL_MIN && fabs(newparam->pdihs.cpB) < GMX_REAL_MIN)
+ {
+ return -1;
+ }
+
+ newparam->pdihs.mult = round_check(old[2], -99, ftype, "multiplicity");
+
+ break;
+ case F_POSRES:
+ newparam->posres.fcA[XX] = old[0];
+ newparam->posres.fcA[YY] = old[1];
+ newparam->posres.fcA[ZZ] = old[2];
+ newparam->posres.fcB[XX] = old[3];
+ newparam->posres.fcB[YY] = old[4];
+ newparam->posres.fcB[ZZ] = old[5];
+ newparam->posres.pos0A[XX] = old[6];
+ newparam->posres.pos0A[YY] = old[7];
+ newparam->posres.pos0A[ZZ] = old[8];
+ newparam->posres.pos0B[XX] = old[9];
+ newparam->posres.pos0B[YY] = old[10];
+ newparam->posres.pos0B[ZZ] = old[11];
+ break;
+ case F_FBPOSRES:
+ newparam->fbposres.geom = round_check(old[0], 0, ftype, "geometry");
+ if (!(newparam->fbposres.geom > efbposresZERO && newparam->fbposres.geom < efbposresNR))
+ {
+ gmx_fatal(FARGS, "Invalid geometry for flat-bottomed position restraint.\n"
+ "Expected number between 1 and %d. Found %d\n", efbposresNR-1,
+ newparam->fbposres.geom);
+ }
+ newparam->fbposres.r = old[1];
+ newparam->fbposres.k = old[2];
+ newparam->fbposres.pos0[XX] = old[3];
+ newparam->fbposres.pos0[YY] = old[4];
+ newparam->fbposres.pos0[ZZ] = old[5];
+ break;
+ case F_DISRES:
+ newparam->disres.label = round_check(old[0], 0, ftype, "label");
+ newparam->disres.type = round_check(old[1], 1, ftype, "type'");
+ newparam->disres.low = old[2];
+ newparam->disres.up1 = old[3];
+ newparam->disres.up2 = old[4];
+ newparam->disres.kfac = old[5];
+ break;
+ case F_ORIRES:
+ newparam->orires.ex = round_check(old[0], 1, ftype, "experiment") - 1;
+ newparam->orires.label = round_check(old[1], 1, ftype, "label");
+ newparam->orires.power = round_check(old[2], 0, ftype, "power");
+ newparam->orires.c = old[3];
+ newparam->orires.obs = old[4];
+ newparam->orires.kfac = old[5];
+ break;
+ case F_DIHRES:
+ newparam->dihres.phiA = old[0];
+ newparam->dihres.dphiA = old[1];
+ newparam->dihres.kfacA = old[2];
+ newparam->dihres.phiB = old[3];
+ newparam->dihres.dphiB = old[4];
+ newparam->dihres.kfacB = old[5];
+ break;
+ case F_RBDIHS:
+ for (i = 0; (i < NR_RBDIHS); i++)
+ {
+ newparam->rbdihs.rbcA[i] = old[i];
+ newparam->rbdihs.rbcB[i] = old[NR_RBDIHS+i];
+ }
+ break;
+ case F_FOURDIHS:
+ /* Read the dihedral parameters to temporary arrays,
+ * and convert them to the computationally faster
+ * Ryckaert-Bellemans form.
+ */
+ /* Use conversion formula for OPLS to Ryckaert-Bellemans: */
+ newparam->rbdihs.rbcA[0] = old[1]+0.5*(old[0]+old[2]);
+ newparam->rbdihs.rbcA[1] = 0.5*(3.0*old[2]-old[0]);
+ newparam->rbdihs.rbcA[2] = 4.0*old[3]-old[1];
+ newparam->rbdihs.rbcA[3] = -2.0*old[2];
+ newparam->rbdihs.rbcA[4] = -4.0*old[3];
+ newparam->rbdihs.rbcA[5] = 0.0;
+
+ newparam->rbdihs.rbcB[0] = old[NR_FOURDIHS+1]+0.5*(old[NR_FOURDIHS+0]+old[NR_FOURDIHS+2]);
+ newparam->rbdihs.rbcB[1] = 0.5*(3.0*old[NR_FOURDIHS+2]-old[NR_FOURDIHS+0]);
+ newparam->rbdihs.rbcB[2] = 4.0*old[NR_FOURDIHS+3]-old[NR_FOURDIHS+1];
+ newparam->rbdihs.rbcB[3] = -2.0*old[NR_FOURDIHS+2];
+ newparam->rbdihs.rbcB[4] = -4.0*old[NR_FOURDIHS+3];
+ newparam->rbdihs.rbcB[5] = 0.0;
+ break;
+ case F_CONSTR:
+ case F_CONSTRNC:
+ newparam->constr.dA = old[0];
+ newparam->constr.dB = old[1];
+ break;
+ case F_SETTLE:
+ newparam->settle.doh = old[0];
+ newparam->settle.dhh = old[1];
+ break;
+ case F_VSITE2:
+ case F_VSITE3:
+ case F_VSITE3FD:
+ case F_VSITE3OUT:
+ case F_VSITE4FD:
+ case F_VSITE4FDN:
+ newparam->vsite.a = old[0];
+ newparam->vsite.b = old[1];
+ newparam->vsite.c = old[2];
+ newparam->vsite.d = old[3];
+ newparam->vsite.e = old[4];
+ newparam->vsite.f = old[5];
+ break;
+ case F_VSITE3FAD:
+ newparam->vsite.a = old[1] * cos(DEG2RAD * old[0]);
+ newparam->vsite.b = old[1] * sin(DEG2RAD * old[0]);
+ newparam->vsite.c = old[2];
+ newparam->vsite.d = old[3];
+ newparam->vsite.e = old[4];
+ newparam->vsite.f = old[5];
+ break;
+ case F_VSITEN:
+ newparam->vsiten.n = round_check(old[0], 1, ftype, "number of atoms");
+ newparam->vsiten.a = old[1];
+ break;
+ case F_CMAP:
+ newparam->cmap.cmapA = old[0];
+ newparam->cmap.cmapB = old[1];
+ break;
+ case F_GB12:
+ case F_GB13:
+ case F_GB14:
+ newparam->gb.sar = old[0];
+ newparam->gb.st = old[1];
+ newparam->gb.pi = old[2];
+ newparam->gb.gbr = old[3];
+ newparam->gb.bmlt = old[4];
+ break;
+ default:
+ gmx_fatal(FARGS, "unknown function type %d in %s line %d",
+ ftype, __FILE__, __LINE__);
}
- break;
- case F_FOURDIHS:
- /* Read the dihedral parameters to temporary arrays,
- * and convert them to the computationally faster
- * Ryckaert-Bellemans form.
- */
- /* Use conversion formula for OPLS to Ryckaert-Bellemans: */
- newparam->rbdihs.rbcA[0]=old[1]+0.5*(old[0]+old[2]);
- newparam->rbdihs.rbcA[1]=0.5*(3.0*old[2]-old[0]);
- newparam->rbdihs.rbcA[2]=4.0*old[3]-old[1];
- newparam->rbdihs.rbcA[3]=-2.0*old[2];
- newparam->rbdihs.rbcA[4]=-4.0*old[3];
- newparam->rbdihs.rbcA[5]=0.0;
-
- newparam->rbdihs.rbcB[0]=old[NR_FOURDIHS+1]+0.5*(old[NR_FOURDIHS+0]+old[NR_FOURDIHS+2]);
- newparam->rbdihs.rbcB[1]=0.5*(3.0*old[NR_FOURDIHS+2]-old[NR_FOURDIHS+0]);
- newparam->rbdihs.rbcB[2]=4.0*old[NR_FOURDIHS+3]-old[NR_FOURDIHS+1];
- newparam->rbdihs.rbcB[3]=-2.0*old[NR_FOURDIHS+2];
- newparam->rbdihs.rbcB[4]=-4.0*old[NR_FOURDIHS+3];
- newparam->rbdihs.rbcB[5]=0.0;
- break;
- case F_CONSTR:
- case F_CONSTRNC:
- newparam->constr.dA = old[0];
- newparam->constr.dB = old[1];
- break;
- case F_SETTLE:
- newparam->settle.doh=old[0];
- newparam->settle.dhh=old[1];
- break;
- case F_VSITE2:
- case F_VSITE3:
- case F_VSITE3FD:
- case F_VSITE3OUT:
- case F_VSITE4FD:
- case F_VSITE4FDN:
- newparam->vsite.a=old[0];
- newparam->vsite.b=old[1];
- newparam->vsite.c=old[2];
- newparam->vsite.d=old[3];
- newparam->vsite.e=old[4];
- newparam->vsite.f=old[5];
- break;
- case F_VSITE3FAD:
- newparam->vsite.a=old[1] * cos(DEG2RAD * old[0]);
- newparam->vsite.b=old[1] * sin(DEG2RAD * old[0]);
- newparam->vsite.c=old[2];
- newparam->vsite.d=old[3];
- newparam->vsite.e=old[4];
- newparam->vsite.f=old[5];
- break;
- case F_VSITEN:
- newparam->vsiten.n = round_check(old[0],1,ftype,"number of atoms");
- newparam->vsiten.a = old[1];
- break;
- case F_CMAP:
- newparam->cmap.cmapA=old[0];
- newparam->cmap.cmapB=old[1];
- break;
- case F_GB12:
- case F_GB13:
- case F_GB14:
- newparam->gb.sar = old[0];
- newparam->gb.st = old[1];
- newparam->gb.pi = old[2];
- newparam->gb.gbr = old[3];
- newparam->gb.bmlt = old[4];
- break;
- default:
- gmx_fatal(FARGS,"unknown function type %d in %s line %d",
- ftype,__FILE__,__LINE__);
- }
return 0;
}
static int enter_params(gmx_ffparams_t *ffparams, t_functype ftype,
- real forceparams[MAXFORCEPARAM],int comb,real reppow,
- int start,gmx_bool bAppend)
+ real forceparams[MAXFORCEPARAM], int comb, real reppow,
+ int start, gmx_bool bAppend)
{
- t_iparams newparam;
- int type;
- int rc;
-
- if( (rc=assign_param(ftype,&newparam,forceparams,comb,reppow))<0 )
- {
- /* -1 means this interaction is all-zero and should not be added */
- return rc;
- }
-
- if (!bAppend) {
- for (type=start; (type<ffparams->ntypes); type++) {
- if (ffparams->functype[type]==ftype) {
- if (F_GB13 == ftype) {
- /* Occasionally, the way the 1-3 reference distance is
- * computed can lead to non-binary-identical results, but I
- * don't know why. */
- if ((gmx_within_tol(newparam.gb.sar, ffparams->iparams[type].gb.sar, 1e-6)) &&
- (gmx_within_tol(newparam.gb.st, ffparams->iparams[type].gb.st, 1e-6)) &&
- (gmx_within_tol(newparam.gb.pi, ffparams->iparams[type].gb.pi, 1e-6)) &&
- (gmx_within_tol(newparam.gb.gbr, ffparams->iparams[type].gb.gbr, 1e-6)) &&
- (gmx_within_tol(newparam.gb.bmlt, ffparams->iparams[type].gb.bmlt, 1e-6))) {
- return type;
- }
- }
- else {
- if (memcmp(&newparam,&ffparams->iparams[type],(size_t)sizeof(newparam)) == 0)
- return type;
- }
- }
+ t_iparams newparam;
+ int type;
+ int rc;
+
+ if ( (rc = assign_param(ftype, &newparam, forceparams, comb, reppow)) < 0)
+ {
+ /* -1 means this interaction is all-zero and should not be added */
+ return rc;
}
- }
- else {
- type = ffparams->ntypes;
- }
- if (debug)
- fprintf(debug,"copying newparam to ffparams->iparams[%d] (ntypes=%d)\n",
- type,ffparams->ntypes);
- memcpy(&ffparams->iparams[type],&newparam,(size_t)sizeof(newparam));
-
- ffparams->ntypes++;
- ffparams->functype[type]=ftype;
-
- return type;
+
+ if (!bAppend)
+ {
+ for (type = start; (type < ffparams->ntypes); type++)
+ {
+ if (ffparams->functype[type] == ftype)
+ {
+ if (F_GB13 == ftype)
+ {
+ /* Occasionally, the way the 1-3 reference distance is
+ * computed can lead to non-binary-identical results, but I
+ * don't know why. */
+ if ((gmx_within_tol(newparam.gb.sar, ffparams->iparams[type].gb.sar, 1e-6)) &&
+ (gmx_within_tol(newparam.gb.st, ffparams->iparams[type].gb.st, 1e-6)) &&
+ (gmx_within_tol(newparam.gb.pi, ffparams->iparams[type].gb.pi, 1e-6)) &&
+ (gmx_within_tol(newparam.gb.gbr, ffparams->iparams[type].gb.gbr, 1e-6)) &&
+ (gmx_within_tol(newparam.gb.bmlt, ffparams->iparams[type].gb.bmlt, 1e-6)))
+ {
+ return type;
+ }
+ }
+ else
+ {
+ if (memcmp(&newparam, &ffparams->iparams[type], (size_t)sizeof(newparam)) == 0)
+ {
+ return type;
+ }
+ }
+ }
+ }
+ }
+ else
+ {
+ type = ffparams->ntypes;
+ }
+ if (debug)
+ {
+ fprintf(debug, "copying newparam to ffparams->iparams[%d] (ntypes=%d)\n",
+ type, ffparams->ntypes);
+ }
+ memcpy(&ffparams->iparams[type], &newparam, (size_t)sizeof(newparam));
+
+ ffparams->ntypes++;
+ ffparams->functype[type] = ftype;
+
+ return type;
}
static void append_interaction(t_ilist *ilist,
- int type,int nral,atom_id a[MAXATOMLIST])
+ int type, int nral, atom_id a[MAXATOMLIST])
{
- int i,where1;
-
- where1 = ilist->nr;
- ilist->nr += nral+1;
-
- ilist->iatoms[where1++]=type;
- for (i=0; (i<nral); i++)
- ilist->iatoms[where1++]=a[i];
+ int i, where1;
+
+ where1 = ilist->nr;
+ ilist->nr += nral+1;
+
+ ilist->iatoms[where1++] = type;
+ for (i = 0; (i < nral); i++)
+ {
+ ilist->iatoms[where1++] = a[i];
+ }
}
-static void enter_function(t_params *p,t_functype ftype,int comb,real reppow,
- gmx_ffparams_t *ffparams,t_ilist *il,
- int *maxtypes,
- gmx_bool bNB,gmx_bool bAppend)
+static void enter_function(t_params *p, t_functype ftype, int comb, real reppow,
+ gmx_ffparams_t *ffparams, t_ilist *il,
+ int *maxtypes,
+ gmx_bool bNB, gmx_bool bAppend)
{
- int k,type,nr,nral,delta,start;
-
- start = ffparams->ntypes;
- nr = p->nr;
-
- for (k=0; k<nr; k++) {
- if (*maxtypes <= ffparams->ntypes) {
- *maxtypes += 1000;
- srenew(ffparams->functype,*maxtypes);
- srenew(ffparams->iparams, *maxtypes);
- if (debug)
- fprintf(debug,"%s, line %d: srenewed idef->functype and idef->iparams to %d\n",
- __FILE__,__LINE__,*maxtypes);
- }
- type = enter_params(ffparams,ftype,p->param[k].c,comb,reppow,start,bAppend);
- /* Type==-1 is used as a signal that this interaction is all-zero and should not be added. */
- if (!bNB && type>=0) {
- nral = NRAL(ftype);
- delta = nr*(nral+1);
- srenew(il->iatoms,il->nr+delta);
- append_interaction(il,type,nral,p->param[k].a);
+ int k, type, nr, nral, delta, start;
+
+ start = ffparams->ntypes;
+ nr = p->nr;
+
+ for (k = 0; k < nr; k++)
+ {
+ if (*maxtypes <= ffparams->ntypes)
+ {
+ *maxtypes += 1000;
+ srenew(ffparams->functype, *maxtypes);
+ srenew(ffparams->iparams, *maxtypes);
+ if (debug)
+ {
+ fprintf(debug, "%s, line %d: srenewed idef->functype and idef->iparams to %d\n",
+ __FILE__, __LINE__, *maxtypes);
+ }
+ }
+ type = enter_params(ffparams, ftype, p->param[k].c, comb, reppow, start, bAppend);
+ /* Type==-1 is used as a signal that this interaction is all-zero and should not be added. */
+ if (!bNB && type >= 0)
+ {
+ nral = NRAL(ftype);
+ delta = nr*(nral+1);
+ srenew(il->iatoms, il->nr+delta);
+ append_interaction(il, type, nral, p->param[k].a);
+ }
}
- }
}
-void convert_params(int atnr,t_params nbtypes[],
- t_molinfo *mi,int comb,double reppow,real fudgeQQ,
- gmx_mtop_t *mtop)
+void convert_params(int atnr, t_params nbtypes[],
+ t_molinfo *mi, int comb, double reppow, real fudgeQQ,
+ gmx_mtop_t *mtop)
{
- int i,j,maxtypes,mt;
- unsigned long flags;
- gmx_ffparams_t *ffp;
- gmx_moltype_t *molt;
- t_params *plist;
-
- maxtypes=0;
-
- ffp = &mtop->ffparams;
- ffp->ntypes = 0;
- ffp->atnr = atnr;
- ffp->functype = NULL;
- ffp->iparams = NULL;
- ffp->reppow = reppow;
-
- enter_function(&(nbtypes[F_LJ]), (t_functype)F_LJ, comb,reppow,ffp,NULL,
- &maxtypes,TRUE,TRUE);
- enter_function(&(nbtypes[F_BHAM]),(t_functype)F_BHAM, comb,reppow,ffp,NULL,
- &maxtypes,TRUE,TRUE);
-
- for(mt=0; mt<mtop->nmoltype; mt++) {
- molt = &mtop->moltype[mt];
- for(i=0; (i<F_NRE); i++) {
- molt->ilist[i].nr = 0;
- molt->ilist[i].iatoms = NULL;
-
- plist = mi[mt].plist;
-
- flags = interaction_function[i].flags;
- if ((i != F_LJ) && (i != F_BHAM) && ((flags & IF_BOND) ||
- (flags & IF_VSITE) ||
- (flags & IF_CONSTRAINT))) {
- enter_function(&(plist[i]),(t_functype)i,comb,reppow,
- ffp,&molt->ilist[i],
- &maxtypes,FALSE,(i == F_POSRES || i == F_FBPOSRES));
- }
+ int i, j, maxtypes, mt;
+ unsigned long flags;
+ gmx_ffparams_t *ffp;
+ gmx_moltype_t *molt;
+ t_params *plist;
+
+ maxtypes = 0;
+
+ ffp = &mtop->ffparams;
+ ffp->ntypes = 0;
+ ffp->atnr = atnr;
+ ffp->functype = NULL;
+ ffp->iparams = NULL;
+ ffp->reppow = reppow;
+
+ enter_function(&(nbtypes[F_LJ]), (t_functype)F_LJ, comb, reppow, ffp, NULL,
+ &maxtypes, TRUE, TRUE);
+ enter_function(&(nbtypes[F_BHAM]), (t_functype)F_BHAM, comb, reppow, ffp, NULL,
+ &maxtypes, TRUE, TRUE);
+
+ for (mt = 0; mt < mtop->nmoltype; mt++)
+ {
+ molt = &mtop->moltype[mt];
+ for (i = 0; (i < F_NRE); i++)
+ {
+ molt->ilist[i].nr = 0;
+ molt->ilist[i].iatoms = NULL;
+
+ plist = mi[mt].plist;
+
+ flags = interaction_function[i].flags;
+ if ((i != F_LJ) && (i != F_BHAM) && ((flags & IF_BOND) ||
+ (flags & IF_VSITE) ||
+ (flags & IF_CONSTRAINT)))
+ {
+ enter_function(&(plist[i]), (t_functype)i, comb, reppow,
+ ffp, &molt->ilist[i],
+ &maxtypes, FALSE, (i == F_POSRES || i == F_FBPOSRES));
+ }
+ }
+ }
+ if (debug)
+ {
+ fprintf(debug, "%s, line %d: There are %d functypes in idef\n",
+ __FILE__, __LINE__, ffp->ntypes);
}
- }
- if (debug) {
- fprintf(debug,"%s, line %d: There are %d functypes in idef\n",
- __FILE__,__LINE__,ffp->ntypes);
- }
- ffp->fudgeQQ = fudgeQQ;
+ ffp->fudgeQQ = fudgeQQ;
}
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff