*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2015,2016,2018, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2016,2018,2019, 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.
#include "gromacs/utility/smalloc.h"
#include "gromacs/utility/txtdump.h"
-static void pr_harm(FILE *fp, const t_iparams *iparams, const char *r, const char *kr)
+static void pr_harm(FILE* fp, const t_iparams* iparams, const char* r, const char* kr)
{
- fprintf(fp, "%sA=%12.5e, %sA=%12.5e, %sB=%12.5e, %sB=%12.5e\n",
- r, iparams->harmonic.rA, kr, iparams->harmonic.krA,
- r, iparams->harmonic.rB, kr, iparams->harmonic.krB);
+ fprintf(fp, "%sA=%12.5e, %sA=%12.5e, %sB=%12.5e, %sB=%12.5e\n", r, iparams->harmonic.rA, kr,
+ iparams->harmonic.krA, r, iparams->harmonic.rB, kr, iparams->harmonic.krB);
}
-void pr_iparams(FILE *fp, t_functype ftype, const t_iparams *iparams)
+void pr_iparams(FILE* fp, t_functype ftype, const t_iparams* iparams)
{
switch (ftype)
{
case F_ANGLES:
- case F_G96ANGLES:
- pr_harm(fp, iparams, "th", "ct");
- break;
+ case F_G96ANGLES: pr_harm(fp, iparams, "th", "ct"); break;
case F_CROSS_BOND_BONDS:
- fprintf(fp, "r1e=%15.8e, r2e=%15.8e, krr=%15.8e\n",
- iparams->cross_bb.r1e, iparams->cross_bb.r2e,
- iparams->cross_bb.krr);
+ fprintf(fp, "r1e=%15.8e, r2e=%15.8e, krr=%15.8e\n", iparams->cross_bb.r1e,
+ iparams->cross_bb.r2e, iparams->cross_bb.krr);
break;
case F_CROSS_BOND_ANGLES:
- fprintf(fp, "r1e=%15.8e, r1e=%15.8e, r3e=%15.8e, krt=%15.8e\n",
- iparams->cross_ba.r1e, iparams->cross_ba.r2e,
- iparams->cross_ba.r3e, iparams->cross_ba.krt);
+ fprintf(fp, "r1e=%15.8e, r1e=%15.8e, r3e=%15.8e, krt=%15.8e\n", iparams->cross_ba.r1e,
+ iparams->cross_ba.r2e, iparams->cross_ba.r3e, iparams->cross_ba.krt);
break;
case F_LINEAR_ANGLES:
- fprintf(fp, "klinA=%15.8e, aA=%15.8e, klinB=%15.8e, aB=%15.8e\n",
- iparams->linangle.klinA, iparams->linangle.aA,
- iparams->linangle.klinB, iparams->linangle.aB);
+ fprintf(fp, "klinA=%15.8e, aA=%15.8e, klinB=%15.8e, aB=%15.8e\n", iparams->linangle.klinA,
+ iparams->linangle.aA, iparams->linangle.klinB, iparams->linangle.aB);
break;
case F_UREY_BRADLEY:
- fprintf(fp, "thetaA=%15.8e, kthetaA=%15.8e, r13A=%15.8e, kUBA=%15.8e, thetaB=%15.8e, kthetaB=%15.8e, r13B=%15.8e, kUBB=%15.8e\n", iparams->u_b.thetaA, iparams->u_b.kthetaA, iparams->u_b.r13A, iparams->u_b.kUBA, iparams->u_b.thetaB, iparams->u_b.kthetaB, iparams->u_b.r13B, iparams->u_b.kUBB);
+ fprintf(fp,
+ "thetaA=%15.8e, kthetaA=%15.8e, r13A=%15.8e, kUBA=%15.8e, thetaB=%15.8e, "
+ "kthetaB=%15.8e, r13B=%15.8e, kUBB=%15.8e\n",
+ iparams->u_b.thetaA, iparams->u_b.kthetaA, iparams->u_b.r13A, iparams->u_b.kUBA,
+ iparams->u_b.thetaB, iparams->u_b.kthetaB, iparams->u_b.r13B, iparams->u_b.kUBB);
break;
case F_QUARTIC_ANGLES:
fprintf(fp, "theta=%15.8e", iparams->qangle.theta);
for (int i = 0; i < 5; i++)
{
- fprintf(fp, ", c%c=%15.8e", '0'+i, iparams->qangle.c[i]);
+ fprintf(fp, ", c%c=%15.8e", '0' + i, iparams->qangle.c[i]);
}
fprintf(fp, "\n");
break;
case F_BHAM:
- fprintf(fp, "a=%15.8e, b=%15.8e, c=%15.8e\n",
- iparams->bham.a, iparams->bham.b, iparams->bham.c);
+ fprintf(fp, "a=%15.8e, b=%15.8e, c=%15.8e\n", iparams->bham.a, iparams->bham.b,
+ iparams->bham.c);
break;
case F_BONDS:
case F_G96BONDS:
- case F_HARMONIC:
- pr_harm(fp, iparams, "b0", "cb");
- break;
- case F_IDIHS:
- pr_harm(fp, iparams, "xi", "cx");
- break;
+ case F_HARMONIC: pr_harm(fp, iparams, "b0", "cb"); break;
+ case F_IDIHS: pr_harm(fp, iparams, "xi", "cx"); break;
case F_MORSE:
- fprintf(fp, "b0A=%15.8e, cbA=%15.8e, betaA=%15.8e, b0B=%15.8e, cbB=%15.8e, betaB=%15.8e\n",
+ fprintf(fp,
+ "b0A=%15.8e, cbA=%15.8e, betaA=%15.8e, b0B=%15.8e, cbB=%15.8e, betaB=%15.8e\n",
iparams->morse.b0A, iparams->morse.cbA, iparams->morse.betaA,
iparams->morse.b0B, iparams->morse.cbB, iparams->morse.betaB);
break;
case F_CUBICBONDS:
- fprintf(fp, "b0=%15.8e, kb=%15.8e, kcub=%15.8e\n",
- iparams->cubic.b0, iparams->cubic.kb, iparams->cubic.kcub);
- break;
- case F_CONNBONDS:
- fprintf(fp, "\n");
+ fprintf(fp, "b0=%15.8e, kb=%15.8e, kcub=%15.8e\n", iparams->cubic.b0, iparams->cubic.kb,
+ iparams->cubic.kcub);
break;
+ case F_CONNBONDS: fprintf(fp, "\n"); break;
case F_FENEBONDS:
fprintf(fp, "bm=%15.8e, kb=%15.8e\n", iparams->fene.bm, iparams->fene.kb);
break;
case F_RESTRBONDS:
- fprintf(fp, "lowA=%15.8e, up1A=%15.8e, up2A=%15.8e, kA=%15.8e, lowB=%15.8e, up1B=%15.8e, up2B=%15.8e, kB=%15.8e,\n",
- iparams->restraint.lowA, iparams->restraint.up1A,
- iparams->restraint.up2A, iparams->restraint.kA,
- iparams->restraint.lowB, iparams->restraint.up1B,
+ fprintf(fp,
+ "lowA=%15.8e, up1A=%15.8e, up2A=%15.8e, kA=%15.8e, lowB=%15.8e, up1B=%15.8e, "
+ "up2B=%15.8e, kB=%15.8e,\n",
+ iparams->restraint.lowA, iparams->restraint.up1A, iparams->restraint.up2A,
+ iparams->restraint.kA, iparams->restraint.lowB, iparams->restraint.up1B,
iparams->restraint.up2B, iparams->restraint.kB);
break;
case F_TABBONDS:
case F_TABBONDSNC:
case F_TABANGLES:
case F_TABDIHS:
- fprintf(fp, "tab=%d, kA=%15.8e, kB=%15.8e\n",
- iparams->tab.table, iparams->tab.kA, iparams->tab.kB);
- break;
- case F_POLARIZATION:
- fprintf(fp, "alpha=%15.8e\n", iparams->polarize.alpha);
+ fprintf(fp, "tab=%d, kA=%15.8e, kB=%15.8e\n", iparams->tab.table, iparams->tab.kA,
+ iparams->tab.kB);
break;
+ case F_POLARIZATION: fprintf(fp, "alpha=%15.8e\n", iparams->polarize.alpha); break;
case F_ANHARM_POL:
- fprintf(fp, "alpha=%15.8e drcut=%15.8e khyp=%15.8e\n",
- iparams->anharm_polarize.alpha,
- iparams->anharm_polarize.drcut,
- iparams->anharm_polarize.khyp);
+ fprintf(fp, "alpha=%15.8e drcut=%15.8e khyp=%15.8e\n", iparams->anharm_polarize.alpha,
+ iparams->anharm_polarize.drcut, iparams->anharm_polarize.khyp);
break;
case F_THOLE_POL:
- fprintf(fp, "a=%15.8e, alpha1=%15.8e, alpha2=%15.8e, rfac=%15.8e\n",
- iparams->thole.a, iparams->thole.alpha1, iparams->thole.alpha2,
- iparams->thole.rfac);
+ fprintf(fp, "a=%15.8e, alpha1=%15.8e, alpha2=%15.8e, rfac=%15.8e\n", iparams->thole.a,
+ iparams->thole.alpha1, iparams->thole.alpha2, iparams->thole.rfac);
break;
case F_WATER_POL:
fprintf(fp, "al_x=%15.8e, al_y=%15.8e, al_z=%15.8e, rOH=%9.6f, rHH=%9.6f, rOD=%9.6f\n",
- iparams->wpol.al_x, iparams->wpol.al_y, iparams->wpol.al_z,
- iparams->wpol.rOH, iparams->wpol.rHH, iparams->wpol.rOD);
- break;
- case F_LJ:
- fprintf(fp, "c6=%15.8e, c12=%15.8e\n", iparams->lj.c6, iparams->lj.c12);
+ iparams->wpol.al_x, iparams->wpol.al_y, iparams->wpol.al_z, iparams->wpol.rOH,
+ iparams->wpol.rHH, iparams->wpol.rOD);
break;
+ case F_LJ: fprintf(fp, "c6=%15.8e, c12=%15.8e\n", iparams->lj.c6, iparams->lj.c12); break;
case F_LJ14:
- fprintf(fp, "c6A=%15.8e, c12A=%15.8e, c6B=%15.8e, c12B=%15.8e\n",
- iparams->lj14.c6A, iparams->lj14.c12A,
- iparams->lj14.c6B, iparams->lj14.c12B);
+ fprintf(fp, "c6A=%15.8e, c12A=%15.8e, c6B=%15.8e, c12B=%15.8e\n", iparams->lj14.c6A,
+ iparams->lj14.c12A, iparams->lj14.c6B, iparams->lj14.c12B);
break;
case F_LJC14_Q:
- fprintf(fp, "fqq=%15.8e, qi=%15.8e, qj=%15.8e, c6=%15.8e, c12=%15.8e\n",
- iparams->ljc14.fqq,
- iparams->ljc14.qi, iparams->ljc14.qj,
- iparams->ljc14.c6, iparams->ljc14.c12);
+ fprintf(fp, "fqq=%15.8e, qi=%15.8e, qj=%15.8e, c6=%15.8e, c12=%15.8e\n", iparams->ljc14.fqq,
+ iparams->ljc14.qi, iparams->ljc14.qj, iparams->ljc14.c6, iparams->ljc14.c12);
break;
case F_LJC_PAIRS_NB:
- fprintf(fp, "qi=%15.8e, qj=%15.8e, c6=%15.8e, c12=%15.8e\n",
- iparams->ljcnb.qi, iparams->ljcnb.qj,
- iparams->ljcnb.c6, iparams->ljcnb.c12);
+ fprintf(fp, "qi=%15.8e, qj=%15.8e, c6=%15.8e, c12=%15.8e\n", iparams->ljcnb.qi,
+ iparams->ljcnb.qj, iparams->ljcnb.c6, iparams->ljcnb.c12);
break;
case F_PDIHS:
case F_PIDIHS:
case F_ANGRES:
case F_ANGRESZ:
fprintf(fp, "phiA=%15.8e, cpA=%15.8e, phiB=%15.8e, cpB=%15.8e, mult=%d\n",
- iparams->pdihs.phiA, iparams->pdihs.cpA,
- iparams->pdihs.phiB, iparams->pdihs.cpB,
- iparams->pdihs.mult);
+ iparams->pdihs.phiA, iparams->pdihs.cpA, iparams->pdihs.phiB,
+ iparams->pdihs.cpB, iparams->pdihs.mult);
break;
case F_DISRES:
fprintf(fp, "label=%4d, type=%1d, low=%15.8e, up1=%15.8e, up2=%15.8e, fac=%15.8e)\n",
- iparams->disres.label, iparams->disres.type,
- iparams->disres.low, iparams->disres.up1,
- iparams->disres.up2, iparams->disres.kfac);
+ iparams->disres.label, iparams->disres.type, iparams->disres.low,
+ iparams->disres.up1, iparams->disres.up2, iparams->disres.kfac);
break;
case F_ORIRES:
fprintf(fp, "ex=%4d, label=%d, power=%4d, c=%15.8e, obs=%15.8e, kfac=%15.8e)\n",
iparams->orires.c, iparams->orires.obs, iparams->orires.kfac);
break;
case F_DIHRES:
- fprintf(fp, "phiA=%15.8e, dphiA=%15.8e, kfacA=%15.8e, phiB=%15.8e, dphiB=%15.8e, kfacB=%15.8e\n",
+ fprintf(fp,
+ "phiA=%15.8e, dphiA=%15.8e, kfacA=%15.8e, phiB=%15.8e, dphiB=%15.8e, "
+ "kfacB=%15.8e\n",
iparams->dihres.phiA, iparams->dihres.dphiA, iparams->dihres.kfacA,
iparams->dihres.phiB, iparams->dihres.dphiB, iparams->dihres.kfacB);
break;
case F_POSRES:
- fprintf(fp, "pos0A=(%15.8e,%15.8e,%15.8e), fcA=(%15.8e,%15.8e,%15.8e), pos0B=(%15.8e,%15.8e,%15.8e), fcB=(%15.8e,%15.8e,%15.8e)\n",
- iparams->posres.pos0A[XX], iparams->posres.pos0A[YY],
- iparams->posres.pos0A[ZZ], iparams->posres.fcA[XX],
- iparams->posres.fcA[YY], iparams->posres.fcA[ZZ],
- iparams->posres.pos0B[XX], iparams->posres.pos0B[YY],
- iparams->posres.pos0B[ZZ], iparams->posres.fcB[XX],
- iparams->posres.fcB[YY], iparams->posres.fcB[ZZ]);
+ fprintf(fp,
+ "pos0A=(%15.8e,%15.8e,%15.8e), fcA=(%15.8e,%15.8e,%15.8e), "
+ "pos0B=(%15.8e,%15.8e,%15.8e), fcB=(%15.8e,%15.8e,%15.8e)\n",
+ iparams->posres.pos0A[XX], iparams->posres.pos0A[YY], iparams->posres.pos0A[ZZ],
+ iparams->posres.fcA[XX], iparams->posres.fcA[YY], iparams->posres.fcA[ZZ],
+ iparams->posres.pos0B[XX], iparams->posres.pos0B[YY], iparams->posres.pos0B[ZZ],
+ iparams->posres.fcB[XX], iparams->posres.fcB[YY], iparams->posres.fcB[ZZ]);
break;
case F_FBPOSRES:
fprintf(fp, "pos0=(%15.8e,%15.8e,%15.8e), geometry=%d, r=%15.8e, k=%15.8e\n",
- iparams->fbposres.pos0[XX], iparams->fbposres.pos0[YY],
- iparams->fbposres.pos0[ZZ], iparams->fbposres.geom,
- iparams->fbposres.r, iparams->fbposres.k);
+ iparams->fbposres.pos0[XX], iparams->fbposres.pos0[YY], iparams->fbposres.pos0[ZZ],
+ iparams->fbposres.geom, iparams->fbposres.r, iparams->fbposres.k);
break;
case F_RBDIHS:
for (int i = 0; i < NR_RBDIHS; i++)
/* Use the OPLS -> Ryckaert-Bellemans formula backwards to get
* the OPLS potential constants back.
*/
- const real *rbcA = iparams->rbdihs.rbcA;
- const real *rbcB = iparams->rbdihs.rbcB;
+ const real* rbcA = iparams->rbdihs.rbcA;
+ const real* rbcB = iparams->rbdihs.rbcB;
real VA[4], VB[4];
- VA[3] = -0.25*rbcA[4];
- VA[2] = -0.5*rbcA[3];
- VA[1] = 4.0*VA[3]-rbcA[2];
- VA[0] = 3.0*VA[2]-2.0*rbcA[1];
+ VA[3] = -0.25 * rbcA[4];
+ VA[2] = -0.5 * rbcA[3];
+ VA[1] = 4.0 * VA[3] - rbcA[2];
+ VA[0] = 3.0 * VA[2] - 2.0 * rbcA[1];
- VB[3] = -0.25*rbcB[4];
- VB[2] = -0.5*rbcB[3];
- VB[1] = 4.0*VB[3]-rbcB[2];
- VB[0] = 3.0*VB[2]-2.0*rbcB[1];
+ VB[3] = -0.25 * rbcB[4];
+ VB[2] = -0.5 * rbcB[3];
+ VB[1] = 4.0 * VB[3] - rbcB[2];
+ VB[0] = 3.0 * VB[2] - 2.0 * rbcB[1];
for (int i = 0; i < NR_FOURDIHS; i++)
{
fprintf(fp, "dA=%15.8e, dB=%15.8e\n", iparams->constr.dA, iparams->constr.dB);
break;
case F_SETTLE:
- fprintf(fp, "doh=%15.8e, dhh=%15.8e\n", iparams->settle.doh,
- iparams->settle.dhh);
- break;
- case F_VSITE2:
- fprintf(fp, "a=%15.8e\n", iparams->vsite.a);
+ fprintf(fp, "doh=%15.8e, dhh=%15.8e\n", iparams->settle.doh, iparams->settle.dhh);
break;
+ case F_VSITE2: fprintf(fp, "a=%15.8e\n", iparams->vsite.a); break;
case F_VSITE3:
case F_VSITE3FD:
case F_VSITE3FAD:
case F_VSITE3OUT:
case F_VSITE4FD:
case F_VSITE4FDN:
- fprintf(fp, "a=%15.8e, b=%15.8e, c=%15.8e\n",
- iparams->vsite.a, iparams->vsite.b, iparams->vsite.c);
+ fprintf(fp, "a=%15.8e, b=%15.8e, c=%15.8e\n", iparams->vsite.a, iparams->vsite.b,
+ iparams->vsite.c);
break;
case F_VSITEN:
fprintf(fp, "n=%2d, a=%15.8e\n", iparams->vsiten.n, iparams->vsiten.a);
case F_CMAP:
fprintf(fp, "cmapA=%1d, cmapB=%1d\n", iparams->cmap.cmapA, iparams->cmap.cmapB);
break;
- case F_RESTRANGLES:
- pr_harm(fp, iparams, "ktheta", "costheta0");
- break;
- case F_RESTRDIHS:
- fprintf(fp, "phiA=%15.8e, cpA=%15.8e",
- iparams->pdihs.phiA, iparams->pdihs.cpA);
+ case F_RESTRANGLES: pr_harm(fp, iparams, "ktheta", "costheta0"); break;
+ case F_RESTRDIHS:
+ fprintf(fp, "phiA=%15.8e, cpA=%15.8e", iparams->pdihs.phiA, iparams->pdihs.cpA);
break;
- case F_CBTDIHS:
+ case F_CBTDIHS:
fprintf(fp, "kphi=%15.8e", iparams->cbtdihs.cbtcA[0]);
for (int i = 1; i < NR_CBTDIHS; i++)
{
- fprintf(fp, ", cbtcA[%d]=%15.8e", i-1, iparams->cbtdihs.cbtcA[i]);
+ fprintf(fp, ", cbtcA[%d]=%15.8e", i - 1, iparams->cbtdihs.cbtcA[i]);
}
fprintf(fp, "\n");
break;
default:
- gmx_fatal(FARGS, "unknown function type %d (%s) in %s line %d",
- ftype, interaction_function[ftype].name, __FILE__, __LINE__);
+ gmx_fatal(FARGS, "unknown function type %d (%s) in %s line %d", ftype,
+ interaction_function[ftype].name, __FILE__, __LINE__);
}
}
-template <typename T>
-static void
-printIlist(FILE *fp, int indent, const char *title,
- const t_functype *functype, const T &ilist,
- gmx_bool bShowNumbers,
- gmx_bool bShowParameters, const t_iparams *iparams)
+template<typename T>
+static void printIlist(FILE* fp,
+ int indent,
+ const char* title,
+ const t_functype* functype,
+ const T& ilist,
+ gmx_bool bShowNumbers,
+ gmx_bool bShowParameters,
+ const t_iparams* iparams)
{
- int i, j, k, type, ftype;
+ int i, j, k, type, ftype;
indent = pr_title(fp, indent, title);
pr_indent(fp, indent);
{
pr_indent(fp, indent);
fprintf(fp, "iatoms:\n");
- for (i = j = 0; i < ilist.size(); )
+ for (i = j = 0; i < ilist.size();)
{
- pr_indent(fp, indent+INDENT);
+ pr_indent(fp, indent + INDENT);
type = ilist.iatoms[i];
ftype = functype[type];
if (bShowNumbers)
if (bShowParameters)
{
fprintf(fp, " ");
- pr_iparams(fp, ftype, &iparams[type]);
+ pr_iparams(fp, ftype, &iparams[type]);
}
fprintf(fp, "\n");
- i += 1+interaction_function[ftype].nratoms;
+ i += 1 + interaction_function[ftype].nratoms;
}
}
}
-void pr_ilist(FILE *fp, int indent, const char *title,
- const t_functype *functype, const InteractionList &ilist,
- gmx_bool bShowNumbers,
- gmx_bool bShowParameters, const t_iparams *iparams)
+void pr_ilist(FILE* fp,
+ int indent,
+ const char* title,
+ const t_functype* functype,
+ const InteractionList& ilist,
+ gmx_bool bShowNumbers,
+ gmx_bool bShowParameters,
+ const t_iparams* iparams)
{
- printIlist(fp, indent, title, functype, ilist,
- bShowNumbers, bShowParameters, iparams);
+ printIlist(fp, indent, title, functype, ilist, bShowNumbers, bShowParameters, iparams);
}
-void pr_idef(FILE *fp, int indent, const char *title, const t_idef *idef,
- gmx_bool bShowNumbers, gmx_bool bShowParameters)
+void pr_idef(FILE* fp, int indent, const char* title, const t_idef* idef, gmx_bool bShowNumbers, gmx_bool bShowParameters)
{
int i, j;
fprintf(fp, "ntypes=%d\n", idef->ntypes);
for (i = 0; i < idef->ntypes; i++)
{
- pr_indent(fp, indent+INDENT);
- fprintf(fp, "functype[%d]=%s, ",
- bShowNumbers ? i : -1,
+ pr_indent(fp, indent + INDENT);
+ fprintf(fp, "functype[%d]=%s, ", bShowNumbers ? i : -1,
interaction_function[idef->functype[i]].name);
pr_iparams(fp, idef->functype[i], &idef->iparams[i]);
}
for (j = 0; (j < F_NRE); j++)
{
- printIlist(fp, indent, interaction_function[j].longname,
- idef->functype, idef->il[j], bShowNumbers,
- bShowParameters, idef->iparams);
+ printIlist(fp, indent, interaction_function[j].longname, idef->functype, idef->il[j],
+ bShowNumbers, bShowParameters, idef->iparams);
}
}
}
-void init_idef(t_idef *idef)
+void init_idef(t_idef* idef)
{
idef->ntypes = 0;
idef->atnr = 0;
idef->ilsort = 0;
}
-void done_idef(t_idef *idef)
+void done_idef(t_idef* idef)
{
sfree(idef->functype);
sfree(idef->iparams);
init_idef(idef);
}
-void copy_ilist(const t_ilist *src, t_ilist *dst)
+void copy_ilist(const t_ilist* src, t_ilist* dst)
{
dst->nr = src->nr;
dst->nr_nonperturbed = src->nr_nonperturbed;