*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2016,2018 by the GROMACS development team.
+ * Copyright (c) 2019,2020,2021, 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 <cstdio>
+#include "gromacs/topology/forcefieldparameters.h"
#include "gromacs/topology/ifunc.h"
#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/smalloc.h"
+#include "gromacs/utility/stringstream.h"
+#include "gromacs/utility/textwriter.h"
#include "gromacs/utility/txtdump.h"
-static void pr_harm(FILE *fp, const t_iparams *iparams, const char *r, const char *kr)
+static void printHarmonicInteraction(gmx::TextWriter* writer,
+ 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);
+ writer->writeLineFormatted("%sA=%12.5e, %sA=%12.5e, %sB=%12.5e, %sB=%12.5e",
+ 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)
+{
+ gmx::StringOutputStream stream;
+ {
+ gmx::TextWriter writer(&stream);
+ printInteractionParameters(&writer, ftype, iparams);
+ }
+ fputs(stream.toString().c_str(), fp);
+}
+
+void printInteractionParameters(gmx::TextWriter* writer, 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: printHarmonicInteraction(writer, 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);
+ writer->writeLineFormatted("r1e=%15.8e, r2e=%15.8e, krr=%15.8e",
+ 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);
+ writer->writeLineFormatted("r1e=%15.8e, r1e=%15.8e, r3e=%15.8e, krt=%15.8e",
+ 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);
+ writer->writeLineFormatted("klinA=%15.8e, aA=%15.8e, klinB=%15.8e, aB=%15.8e",
+ 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);
+ writer->writeLineFormatted(
+ "thetaA=%15.8e, kthetaA=%15.8e, r13A=%15.8e, kUBA=%15.8e, thetaB=%15.8e, "
+ "kthetaB=%15.8e, r13B=%15.8e, kUBB=%15.8e",
+ 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);
+ writer->writeStringFormatted("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]);
+ writer->writeStringFormatted(", c%c=%15.8e", '0' + i, iparams.qangle.c[i]);
}
- fprintf(fp, "\n");
+ writer->ensureLineBreak();
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);
+ writer->writeLineFormatted(
+ "a=%15.8e, b=%15.8e, c=%15.8e", 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: printHarmonicInteraction(writer, iparams, "b0", "cb"); break;
+ case F_IDIHS: printHarmonicInteraction(writer, 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",
- iparams->morse.b0A, iparams->morse.cbA, iparams->morse.betaA,
- iparams->morse.b0B, iparams->morse.cbB, iparams->morse.betaB);
+ writer->writeLineFormatted(
+ "b0A=%15.8e, cbA=%15.8e, betaA=%15.8e, b0B=%15.8e, cbB=%15.8e, betaB=%15.8e",
+ 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");
+ writer->writeLineFormatted("b0=%15.8e, kb=%15.8e, kcub=%15.8e",
+ iparams.cubic.b0,
+ iparams.cubic.kb,
+ iparams.cubic.kcub);
break;
+ case F_CONNBONDS: writer->ensureEmptyLine(); break;
case F_FENEBONDS:
- fprintf(fp, "bm=%15.8e, kb=%15.8e\n", iparams->fene.bm, iparams->fene.kb);
+ writer->writeLineFormatted("bm=%15.8e, kb=%15.8e", 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,
- iparams->restraint.up2B, iparams->restraint.kB);
+ writer->writeLineFormatted(
+ "lowA=%15.8e, up1A=%15.8e, up2A=%15.8e, kA=%15.8e, lowB=%15.8e, up1B=%15.8e, "
+ "up2B=%15.8e, kB=%15.8e,",
+ 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);
+ writer->writeLineFormatted(
+ "tab=%d, kA=%15.8e, kB=%15.8e", iparams.tab.table, iparams.tab.kA, iparams.tab.kB);
break;
case F_POLARIZATION:
- fprintf(fp, "alpha=%15.8e\n", iparams->polarize.alpha);
+ writer->writeLineFormatted("alpha=%15.8e", 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);
+ writer->writeLineFormatted("alpha=%15.8e drcut=%15.8e khyp=%15.8e",
+ 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);
+ writer->writeLineFormatted("a=%15.8e, alpha1=%15.8e, alpha2=%15.8e",
+ iparams.thole.a,
+ iparams.thole.alpha1,
+ iparams.thole.alpha2);
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);
+ writer->writeLineFormatted(
+ "al_x=%15.8e, al_y=%15.8e, al_z=%15.8e, rOH=%9.6f, rHH=%9.6f, rOD=%9.6f",
+ 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);
+ writer->writeLineFormatted("c6=%15.8e, c12=%15.8e", 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);
+ writer->writeLineFormatted("c6A=%15.8e, c12A=%15.8e, c6B=%15.8e, c12B=%15.8e",
+ 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);
+ writer->writeLineFormatted("fqq=%15.8e, qi=%15.8e, qj=%15.8e, c6=%15.8e, c12=%15.8e",
+ 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);
+ writer->writeLineFormatted("qi=%15.8e, qj=%15.8e, c6=%15.8e, c12=%15.8e",
+ 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);
+ writer->writeLineFormatted("phiA=%15.8e, cpA=%15.8e, phiB=%15.8e, cpB=%15.8e, mult=%d",
+ 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);
+ writer->writeLineFormatted(
+ "label=%4d, type=%1d, low=%15.8e, up1=%15.8e, up2=%15.8e, fac=%15.8e)",
+ 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.ex, iparams->orires.label, iparams->orires.power,
- iparams->orires.c, iparams->orires.obs, iparams->orires.kfac);
+ writer->writeLineFormatted(
+ "ex=%4d, label=%d, power=%4d, c=%15.8e, obs=%15.8e, kfac=%15.8e)",
+ iparams.orires.ex,
+ iparams.orires.label,
+ iparams.orires.power,
+ 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",
- iparams->dihres.phiA, iparams->dihres.dphiA, iparams->dihres.kfacA,
- iparams->dihres.phiB, iparams->dihres.dphiB, iparams->dihres.kfacB);
+ writer->writeLineFormatted(
+ "phiA=%15.8e, dphiA=%15.8e, kfacA=%15.8e, phiB=%15.8e, dphiB=%15.8e, "
+ "kfacB=%15.8e",
+ 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]);
+ writer->writeLineFormatted(
+ "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)",
+ 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);
+ writer->writeLineFormatted(
+ "pos0=(%15.8e,%15.8e,%15.8e), geometry=%d, r=%15.8e, k=%15.8e",
+ 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++)
{
- fprintf(fp, "%srbcA[%d]=%15.8e", i == 0 ? "" : ", ", i, iparams->rbdihs.rbcA[i]);
+ writer->writeStringFormatted(
+ "%srbcA[%d]=%15.8e", i == 0 ? "" : ", ", i, iparams.rbdihs.rbcA[i]);
}
- fprintf(fp, "\n");
+ writer->ensureLineBreak();
for (int i = 0; i < NR_RBDIHS; i++)
{
- fprintf(fp, "%srbcB[%d]=%15.8e", i == 0 ? "" : ", ", i, iparams->rbdihs.rbcB[i]);
+ writer->writeStringFormatted(
+ "%srbcB[%d]=%15.8e", i == 0 ? "" : ", ", i, iparams.rbdihs.rbcB[i]);
}
- fprintf(fp, "\n");
+ writer->ensureLineBreak();
break;
case F_FOURDIHS:
{
/* 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, "%sFourA[%d]=%15.8e", i == 0 ? "" : ", ", i, VA[i]);
+ writer->writeStringFormatted("%sFourA[%d]=%15.8e", i == 0 ? "" : ", ", i, VA[i]);
}
- fprintf(fp, "\n");
+ writer->ensureLineBreak();
for (int i = 0; i < NR_FOURDIHS; i++)
{
- fprintf(fp, "%sFourB[%d]=%15.8e", i == 0 ? "" : ", ", i, VB[i]);
+ writer->writeStringFormatted("%sFourB[%d]=%15.8e", i == 0 ? "" : ", ", i, VB[i]);
}
- fprintf(fp, "\n");
+ writer->ensureLineBreak();
break;
}
case F_CONSTR:
case F_CONSTRNC:
- fprintf(fp, "dA=%15.8e, dB=%15.8e\n", iparams->constr.dA, iparams->constr.dB);
+ writer->writeLineFormatted("dA=%15.8e, dB=%15.8e", 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);
+ writer->writeLineFormatted("doh=%15.8e, dhh=%15.8e", iparams.settle.doh, iparams.settle.dhh);
break;
+ case F_VSITE1: writer->ensureEmptyLine(); break;
+ case F_VSITE2: writer->writeLineFormatted("a=%15.8e", iparams.vsite.a); break;
case F_VSITE3:
case F_VSITE3FD:
case F_VSITE3FAD:
- fprintf(fp, "a=%15.8e, b=%15.8e\n", iparams->vsite.a, iparams->vsite.b);
+ writer->writeLineFormatted("a=%15.8e, b=%15.8e", iparams.vsite.a, iparams.vsite.b);
break;
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);
+ writer->writeLineFormatted(
+ "a=%15.8e, b=%15.8e, c=%15.8e", 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);
+ writer->writeLineFormatted("n=%2d, a=%15.8e", iparams.vsiten.n, iparams.vsiten.a);
break;
- case F_GB12:
- case F_GB13:
- case F_GB14:
- fprintf(fp, "sar=%15.8e, st=%15.8e, pi=%15.8e, gbr=%15.8e, bmlt=%15.8e\n", iparams->gb.sar, iparams->gb.st, iparams->gb.pi, iparams->gb.gbr, iparams->gb.bmlt);
+ case F_GB12_NOLONGERUSED:
+ case F_GB13_NOLONGERUSED:
+ case F_GB14_NOLONGERUSED:
+ // These could only be generated by grompp, not written in
+ // a .top file. Now that implicit solvent is not
+ // supported, they can't be generated, and the values are
+ // ignored if read from an old .tpr file. So there is
+ // nothing to print.
break;
case F_CMAP:
- fprintf(fp, "cmapA=%1d, cmapB=%1d\n", iparams->cmap.cmapA, iparams->cmap.cmapB);
+ writer->writeLineFormatted("cmapA=%1d, cmapB=%1d", iparams.cmap.cmapA, iparams.cmap.cmapB);
break;
- case F_RESTRANGLES:
- pr_harm(fp, iparams, "ktheta", "costheta0");
+ case F_RESTRANGLES: printHarmonicInteraction(writer, iparams, "ktheta", "costheta0"); break;
+ case F_RESTRDIHS:
+ writer->writeLineFormatted("phiA=%15.8e, cpA=%15.8e", iparams.pdihs.phiA, iparams.pdihs.cpA);
break;
- case F_RESTRDIHS:
- fprintf(fp, "phiA=%15.8e, cpA=%15.8e",
- iparams->pdihs.phiA, iparams->pdihs.cpA);
- break;
- case F_CBTDIHS:
- fprintf(fp, "kphi=%15.8e", iparams->cbtdihs.cbtcA[0]);
+ case F_CBTDIHS:
+ writer->writeLineFormatted("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]);
+ writer->writeStringFormatted(", cbtcA[%d]=%15.8e", i - 1, iparams.cbtdihs.cbtcA[i]);
}
- fprintf(fp, "\n");
+ writer->ensureLineBreak();
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__);
}
}
-void pr_ilist(FILE *fp, int indent, const char *title,
- const t_functype *functype, const t_ilist *ilist, gmx_bool bShowNumbers)
+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;
- t_iatom *iatoms;
-
- if (available(fp, ilist, indent, title) && ilist->nr > 0)
+ indent = pr_title(fp, indent, title);
+ pr_indent(fp, indent);
+ fprintf(fp, "nr: %d\n", ilist.size());
+ if (!ilist.empty())
{
- indent = pr_title(fp, indent, title);
pr_indent(fp, indent);
- fprintf(fp, "nr: %d\n", ilist->nr);
- if (ilist->nr > 0)
+ fprintf(fp, "iatoms:\n");
+ int j = 0;
+ for (int i = 0; i < ilist.size();)
{
- pr_indent(fp, indent);
- fprintf(fp, "iatoms:\n");
- iatoms = ilist->iatoms;
- for (i = j = 0; i < ilist->nr; )
+ pr_indent(fp, indent + INDENT);
+ const int type = ilist.iatoms[i];
+ const int ftype = functype[type];
+ if (bShowNumbers)
{
-#ifndef DEBUG
- pr_indent(fp, indent+INDENT);
- type = *(iatoms++);
- ftype = functype[type];
- fprintf(fp, "%d type=%d (%s)",
- bShowNumbers ? j : -1, bShowNumbers ? type : -1,
- interaction_function[ftype].name);
- j++;
- for (k = 0; k < interaction_function[ftype].nratoms; k++)
- {
- fprintf(fp, " %d", *(iatoms++));
- }
- fprintf(fp, "\n");
- i += 1+interaction_function[ftype].nratoms;
-#else
- fprintf(fp, "%5d%5d\n", i, iatoms[i]);
- i++;
-#endif
+ fprintf(fp, "%d type=%d ", j, type);
}
- }
- }
-}
-
-static void pr_cmap(FILE *fp, int indent, const char *title,
- const gmx_cmap_t *cmap_grid, gmx_bool bShowNumbers)
-{
- int i, j, nelem;
- real dx, idx;
-
- dx = 360.0 / cmap_grid->grid_spacing;
- nelem = cmap_grid->grid_spacing*cmap_grid->grid_spacing;
-
- if (available(fp, cmap_grid, indent, title))
- {
- fprintf(fp, "%s\n", title);
-
- for (i = 0; i < cmap_grid->ngrid; i++)
- {
- idx = -180.0;
- fprintf(fp, "%8s %8s %8s %8s\n", "V", "dVdx", "dVdy", "d2dV");
-
- fprintf(fp, "grid[%3d]={\n", bShowNumbers ? i : -1);
-
- for (j = 0; j < nelem; j++)
+ j++;
+ printf("(%s)", interaction_function[ftype].name);
+ for (int k = 0; k < interaction_function[ftype].nratoms; k++)
{
- if ( (j%cmap_grid->grid_spacing) == 0)
- {
- fprintf(fp, "%8.1f\n", idx);
- idx += dx;
- }
-
- fprintf(fp, "%8.3f ", cmap_grid->cmapdata[i].cmap[j*4]);
- fprintf(fp, "%8.3f ", cmap_grid->cmapdata[i].cmap[j*4+1]);
- fprintf(fp, "%8.3f ", cmap_grid->cmapdata[i].cmap[j*4+2]);
- fprintf(fp, "%8.3f\n", cmap_grid->cmapdata[i].cmap[j*4+3]);
+ fprintf(fp, " %3d", ilist.iatoms[i + 1 + k]);
+ }
+ if (bShowParameters)
+ {
+ fprintf(fp, " ");
+ pr_iparams(fp, ftype, iparams[type]);
}
fprintf(fp, "\n");
+ i += 1 + interaction_function[ftype].nratoms;
}
}
-
}
-void pr_ffparams(FILE *fp, int indent, const char *title,
- const gmx_ffparams_t *ffparams,
- gmx_bool bShowNumbers)
+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)
{
- int i;
-
- indent = pr_title(fp, indent, title);
- pr_indent(fp, indent);
- fprintf(fp, "atnr=%d\n", ffparams->atnr);
- pr_indent(fp, indent);
- fprintf(fp, "ntypes=%d\n", ffparams->ntypes);
- for (i = 0; i < ffparams->ntypes; i++)
- {
- pr_indent(fp, indent+INDENT);
- fprintf(fp, "functype[%d]=%s, ",
- bShowNumbers ? i : -1,
- interaction_function[ffparams->functype[i]].name);
- pr_iparams(fp, ffparams->functype[i], &ffparams->iparams[i]);
- }
- pr_double(fp, indent, "reppow", ffparams->reppow);
- pr_real(fp, indent, "fudgeQQ", ffparams->fudgeQQ);
- pr_cmap(fp, indent, "cmap", &ffparams->cmap_grid, bShowNumbers);
+ 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)
+void pr_idef(FILE* fp, int indent, const char* title, const t_idef* idef, gmx_bool bShowNumbers, gmx_bool bShowParameters)
{
- int i, j;
-
if (available(fp, idef, indent, title))
{
indent = pr_title(fp, indent, title);
fprintf(fp, "atnr=%d\n", idef->atnr);
pr_indent(fp, indent);
fprintf(fp, "ntypes=%d\n", idef->ntypes);
- for (i = 0; i < idef->ntypes; i++)
+ for (int i = 0; i < idef->ntypes; i++)
{
- pr_indent(fp, indent+INDENT);
- fprintf(fp, "functype[%d]=%s, ",
+ 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]);
+ pr_iparams(fp, idef->functype[i], idef->iparams[i]);
}
pr_real(fp, indent, "fudgeQQ", idef->fudgeQQ);
- for (j = 0; (j < F_NRE); j++)
+ for (int j = 0; (j < F_NRE); j++)
{
- pr_ilist(fp, indent, interaction_function[j].longname,
- idef->functype, &idef->il[j], bShowNumbers);
+ printIlist(fp,
+ indent,
+ interaction_function[j].longname,
+ idef->functype,
+ idef->il[j],
+ bShowNumbers,
+ bShowParameters,
+ idef->iparams);
}
}
}
+
+void init_idef(t_idef* idef)
+{
+ idef->ntypes = 0;
+ idef->atnr = 0;
+ idef->functype = nullptr;
+ idef->iparams = nullptr;
+ idef->fudgeQQ = 0.0;
+ idef->iparams_posres = nullptr;
+ idef->iparams_fbposres = nullptr;
+ for (int f = 0; f < F_NRE; ++f)
+ {
+ idef->il[f].iatoms = nullptr;
+ idef->il[f].nalloc = 0;
+ idef->il[f].nr = 0;
+ }
+}
+
+InteractionDefinitions::InteractionDefinitions(const gmx_ffparams_t& ffparams) :
+ iparams(ffparams.iparams), functype(ffparams.functype), cmap_grid(ffparams.cmap_grid)
+{
+}
+
+void InteractionDefinitions::clear()
+{
+ /* Clear the counts */
+ for (auto& ilist : il)
+ {
+ ilist.clear();
+ }
+ iparams_posres.clear();
+ iparams_fbposres.clear();
+}
+
+void done_idef(t_idef* idef)
+{
+ sfree(idef->functype);
+ sfree(idef->iparams);
+ sfree(idef->iparams_posres);
+ sfree(idef->iparams_fbposres);
+ for (int f = 0; f < F_NRE; ++f)
+ {
+ sfree(idef->il[f].iatoms);
+ }
+
+ init_idef(idef);
+}
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff