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patch-v2019.4
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patch-v2019.4
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patch -p 1 << EOF
diff --git a/src/gromacs/gmxpreprocess/readir.cpp b/src/gromacs/gmxpreprocess/readir.cpp
index 6b82ca99b2..6855a15494 100644
--- a/src/gromacs/gmxpreprocess/readir.cpp
+++ b/src/gromacs/gmxpreprocess/readir.cpp
@@ -1026,7 +1026,7 @@ void check_ir(const char *mdparin, t_inputrec *ir, t_gromppopts *opts,
{
if (ir->epc > epcNO)
{
- if ((ir->epc != epcBERENDSEN) && (ir->epc != epcMTTK))
+ if ((ir->epc != epcBERENDSEN) && (ir->epc != epcMTTK) && (ir->epc != epcCRESCALE))
{
warning_error(wi, "for md-vv and md-vv-avek, can only use Berendsen and Martyna-Tuckerman-Tobias-Klein (MTTK) equations for pressure control; MTTK is equivalent to Parrinello-Rahman.");
}
diff --git a/src/gromacs/mdlib/coupling.cpp b/src/gromacs/mdlib/coupling.cpp
index 5927ace633..31ac1264a9 100644
--- a/src/gromacs/mdlib/coupling.cpp
+++ b/src/gromacs/mdlib/coupling.cpp
@@ -736,6 +736,242 @@ void berendsen_pscale(const t_inputrec *ir, const matrix mu,
inc_nrnb(nrnb, eNR_PCOUPL, nr_atoms);
}
+void crescale_pcoupl(FILE *fplog, int64_t step,
+ const t_inputrec *ir, real dt,
+ const tensor pres, const matrix box,
+ const matrix force_vir, const matrix constraint_vir,
+ matrix mu, double *baros_integral)
+{
+ int d, n;
+ real scalar_pressure, xy_pressure, p_corr_z;
+ char buf[STRLEN];
+
+ /*
+ * Calculate the scaling matrix mu
+ */
+ scalar_pressure = 0;
+ xy_pressure = 0;
+ for (d = 0; d < DIM; d++)
+ {
+ scalar_pressure += pres[d][d]/DIM;
+ if (d != ZZ)
+ {
+ xy_pressure += pres[d][d]/(DIM-1);
+ }
+ }
+ /* Pressure is now in bar, everywhere. */
+#define factor(d, m) (ir->compress[d][m]*dt/ir->tau_p)
+
+ /* mu has been changed from pow(1+...,1/3) to 1+.../3, since this is
+ * necessary for triclinic scaling
+ */
+ clear_mat(mu);
+
+ /* C-RESCALE */
+ // seed hardcoded to zero now
+ gmx::ThreeFry2x64<64> rng(0, gmx::RandomDomain::Barostat);
+ gmx::NormalDistribution<real> normalDist;
+ rng.restart(step, 0);
+ real vol=1.0;
+ for (d = 0; d < DIM; d++) vol*=box[d][d];
+ real gauss;
+ real gauss2;
+ real kt;
+ real depsilon, dsigma;
+ kt=ir->opts.ref_t[0]*BOLTZ;
+ if(kt<0.0) kt=0.0;
+ /* END C-RESCALE */
+
+ switch (ir->epct)
+ {
+ case epctISOTROPIC:
+ /* C-RESCALE */
+ gauss=normalDist(rng);
+ vol=1.0; for (d = 0; d < DIM; d++) vol*=box[d][d];
+ /* END C-RESCALE */
+ for (d = 0; d < DIM; d++)
+ {
+ /* Berendsen: */
+ /* mu[d][d] = 1.0 - factor(d, d)*(ir->ref_p[d][d] - scalar_pressure) /DIM; */
+ /* C-RESCALE */
+ mu[d][d] = exp(- factor(d, d)*(ir->ref_p[d][d] - scalar_pressure) /DIM +
+ sqrt(2.0*kt*factor(d, d)*PRESFAC/vol)*gauss/DIM);
+ }
+ break;
+ case epctSEMIISOTROPIC:
+ /* C-RESCALE */
+ gauss=normalDist(rng);
+ gauss2=normalDist(rng);
+ vol=1.0; for (d = 0; d < DIM; d++) vol*=box[d][d];
+ for (d = 0; d < ZZ; d++)
+ {
+ /* Berendsen: */
+ /* mu[d][d] = 1.0 - factor(d, d)*(ir->ref_p[d][d]-xy_pressure)/DIM; */
+ /* C-RESCALE */
+ mu[d][d] = exp(- factor(d, d)*(ir->ref_p[d][d] - xy_pressure) /DIM +
+ sqrt((DIM-1)*2.0*kt*factor(d, d)*PRESFAC/vol/DIM)/(DIM-1)*gauss);
+ }
+ /* Notice: we here allow ir->ref_p[ZZ][ZZ] != ir->ref_p[d][d] although this is not well defined */
+ /* Berendsen: 1.0 - factor(ZZ, ZZ)*(ir->ref_p[ZZ][ZZ] - pres[ZZ][ZZ])/DIM; */
+ mu[ZZ][ZZ] = exp(- factor(ZZ, ZZ)*(ir->ref_p[ZZ][ZZ] - pres[ZZ][ZZ]) /DIM +
+ sqrt(2.0*kt*factor(d, d)*PRESFAC/vol/DIM)*gauss2);
+ break;
+#if 0
+ case epctANISOTROPIC:
+ for (d = 0; d < DIM; d++)
+ {
+ for (n = 0; n < DIM; n++)
+ {
+ mu[d][n] = (d == n ? 1.0 : 0.0)
+ -factor(d, n)*(ir->ref_p[d][n] - pres[d][n])/DIM;
+ }
+ }
+ break;
+#endif
+ case epctSURFACETENSION:
+ /* C-RESCALE */
+ gauss=normalDist(rng);
+ gauss2=normalDist(rng);
+ vol=1.0; for (d = 0; d < DIM; d++) vol*=box[d][d];
+ for (d = 0; d < ZZ; d++)
+ {
+ /* Notice: we here use ref_p[ZZ][ZZ] as isotropic pressure and ir->ref_p[d][d] as surface tension */
+ mu[d][d] = exp(- factor(d, d)*(ir->ref_p[ZZ][ZZ]-ir->ref_p[d][d]/box[ZZ][ZZ] - xy_pressure) /DIM +
+ sqrt(4.0/3.0*kt*factor(d, d)*PRESFAC/vol)/(DIM-1)*gauss);
+ }
+ mu[ZZ][ZZ] = exp(- factor(ZZ, ZZ)*(ir->ref_p[ZZ][ZZ] - pres[ZZ][ZZ]) /DIM +
+ sqrt(2.0/3.0*kt*factor(d, d)*PRESFAC/vol)*gauss2);
+ break;
+ default:
+ gmx_fatal(FARGS, "Berendsen pressure coupling type %s not supported yet\n",
+ EPCOUPLTYPETYPE(ir->epct));
+ }
+ /* To fullfill the orientation restrictions on triclinic boxes
+ * we will set mu_yx, mu_zx and mu_zy to 0 and correct
+ * the other elements of mu to first order.
+ */
+ mu[YY][XX] += mu[XX][YY];
+ mu[ZZ][XX] += mu[XX][ZZ];
+ mu[ZZ][YY] += mu[YY][ZZ];
+ mu[XX][YY] = 0;
+ mu[XX][ZZ] = 0;
+ mu[YY][ZZ] = 0;
+
+ /* Keep track of the work the barostat applies on the system.
+ * Without constraints force_vir tells us how Epot changes when scaling.
+ * With constraints constraint_vir gives us the constraint contribution
+ * to both Epot and Ekin. Although we are not scaling velocities, scaling
+ * the coordinates leads to scaling of distances involved in constraints.
+ * This in turn changes the angular momentum (even if the constrained
+ * distances are corrected at the next step). The kinetic component
+ * of the constraint virial captures the angular momentum change.
+ */
+ for (int d = 0; d < DIM; d++)
+ {
+ for (int n = 0; n <= d; n++)
+ {
+ *baros_integral -= 2*(mu[d][n] - (n == d ? 1 : 0))*(force_vir[d][n] + constraint_vir[d][n]);
+ }
+ }
+
+ if (debug)
+ {
+ pr_rvecs(debug, 0, "PC: pres ", pres, 3);
+ pr_rvecs(debug, 0, "PC: mu ", mu, 3);
+ }
+
+ if (mu[XX][XX] < 0.99 || mu[XX][XX] > 1.01 ||
+ mu[YY][YY] < 0.99 || mu[YY][YY] > 1.01 ||
+ mu[ZZ][ZZ] < 0.99 || mu[ZZ][ZZ] > 1.01)
+ {
+ char buf2[22];
+ sprintf(buf, "\nStep %s Warning: pressure scaling more than 1%%, "
+ "mu: %g %g %g\n",
+ gmx_step_str(step, buf2), mu[XX][XX], mu[YY][YY], mu[ZZ][ZZ]);
+ if (fplog)
+ {
+ fprintf(fplog, "%s", buf);
+ }
+ fprintf(stderr, "%s", buf);
+ }
+}
+
+void crescale_pscale(const t_inputrec *ir, const matrix mu,
+ matrix box, matrix box_rel,
+ int start, int nr_atoms,
+ rvec x[], rvec v[], const unsigned short cFREEZE[],
+ t_nrnb *nrnb)
+{
+ ivec *nFreeze = ir->opts.nFreeze;
+ int n, d;
+ int nthreads gmx_unused;
+ matrix inv_mu;
+
+#ifndef __clang_analyzer__
+ nthreads = gmx_omp_nthreads_get(emntUpdate);
+#endif
+
+ /* find the inverse matrix */
+ inv_mu[XX][XX]=1.0/mu[XX][XX];
+ inv_mu[YY][YY]=1.0/mu[YY][YY];
+ inv_mu[ZZ][ZZ]=1.0/mu[ZZ][ZZ];
+
+ inv_mu[YY][XX]=-mu[YY][XX]/(mu[XX][XX]*mu[YY][YY]);
+ inv_mu[YY][ZZ]=-mu[YY][ZZ]/(mu[YY][YY]*mu[ZZ][ZZ]);
+ inv_mu[ZZ][XX]=(mu[YY][XX]*mu[YY][ZZ] - mu[YY][YY]*mu[ZZ][XX]) / (mu[XX][XX]*mu[YY][YY]*mu[ZZ][ZZ]);
+
+ inv_mu[XX][YY]=0.0;
+ inv_mu[ZZ][YY]=0.0;
+ inv_mu[ZZ][XX]=0.0;
+
+ /* Scale the positions and the velocities */
+#pragma omp parallel for num_threads(nthreads) schedule(static)
+ for (n = start; n < start+nr_atoms; n++)
+ {
+ // Trivial OpenMP region that does not throw
+ int g;
+
+ if (cFREEZE == nullptr)
+ {
+ g = 0;
+ }
+ else
+ {
+ g = cFREEZE[n];
+ }
+
+ if (!nFreeze[g][XX])
+ {
+ x[n][XX] = mu[XX][XX]*x[n][XX]+mu[YY][XX]*x[n][YY]+mu[ZZ][XX]*x[n][ZZ];
+ v[n][XX] = inv_mu[XX][XX]*v[n][XX]+inv_mu[YY][XX]*v[n][YY]+inv_mu[ZZ][XX]*v[n][ZZ];
+ }
+ if (!nFreeze[g][YY])
+ {
+ x[n][YY] = mu[YY][YY]*x[n][YY]+mu[ZZ][YY]*x[n][ZZ];
+ v[n][YY] = inv_mu[YY][YY]*v[n][YY]+inv_mu[ZZ][YY]*v[n][ZZ];
+ }
+ if (!nFreeze[g][ZZ])
+ {
+ x[n][ZZ] = mu[ZZ][ZZ]*x[n][ZZ];
+ v[n][ZZ] = inv_mu[ZZ][ZZ]*v[n][ZZ];
+ }
+ }
+ /* compute final boxlengths */
+ for (d = 0; d < DIM; d++)
+ {
+ box[d][XX] = mu[XX][XX]*box[d][XX]+mu[YY][XX]*box[d][YY]+mu[ZZ][XX]*box[d][ZZ];
+ box[d][YY] = mu[YY][YY]*box[d][YY]+mu[ZZ][YY]*box[d][ZZ];
+ box[d][ZZ] = mu[ZZ][ZZ]*box[d][ZZ];
+ }
+
+ preserve_box_shape(ir, box_rel, box);
+
+ /* (un)shifting should NOT be done after this,
+ * since the box vectors might have changed
+ */
+ inc_nrnb(nrnb, eNR_PCOUPL, nr_atoms);
+}
+
void berendsen_tcoupl(const t_inputrec *ir, const gmx_ekindata_t *ekind, real dt,
std::vector<double> &therm_integral)
{
@@ -1405,6 +1641,9 @@ real NPT_energy(const t_inputrec *ir, const t_state *state, const t_extmass *Mas
case epcBERENDSEN:
energyNPT += state->baros_integral;
break;
+ case epcCRESCALE:
+ energyNPT += state->baros_integral;
+ break;
default:
GMX_RELEASE_ASSERT(false, "Conserved energy quantity for pressure coupling is not handled. A case should be added with either the conserved quantity added or nothing added and an exclusion added to integratorHasConservedEnergyQuantity().");
}
diff --git a/src/gromacs/mdlib/update.cpp b/src/gromacs/mdlib/update.cpp
index af0e485c75..ad3295efe6 100644
--- a/src/gromacs/mdlib/update.cpp
+++ b/src/gromacs/mdlib/update.cpp
@@ -1721,6 +1721,21 @@ void update_pcouple_after_coordinates(FILE *fplog,
md->cFREEZE, nrnb);
}
break;
+ case (epcCRESCALE):
+ if (isPressureCouplingStep(step, inputrec))
+ {
+ real dtpc = inputrec->nstpcouple*dt;
+ matrix mu;
+ crescale_pcoupl(fplog, step, inputrec, dtpc,
+ pressure, state->box,
+ forceVirial, constraintVirial,
+ mu, &state->baros_integral);
+ crescale_pscale(inputrec, mu, state->box, state->box_rel,
+ start, homenr, state->x.rvec_array(),
+ state->v.rvec_array(),
+ md->cFREEZE, nrnb);
+ }
+ break;
case (epcPARRINELLORAHMAN):
if (isPressureCouplingStep(step, inputrec))
{
diff --git a/src/gromacs/mdlib/update.h b/src/gromacs/mdlib/update.h
index 81b1ace278..fa905622ce 100644
--- a/src/gromacs/mdlib/update.h
+++ b/src/gromacs/mdlib/update.h
@@ -278,6 +278,18 @@ void berendsen_pscale(const t_inputrec *ir, const matrix mu,
rvec x[], const unsigned short cFREEZE[],
t_nrnb *nrnb);
+void crescale_pcoupl(FILE *fplog, int64_t step,
+ const t_inputrec *ir, real dt,
+ const tensor pres, const matrix box,
+ const matrix force_vir, const matrix constraint_vir,
+ matrix mu, double *baros_integral);
+
+void crescale_pscale(const t_inputrec *ir, const matrix mu,
+ matrix box, matrix box_rel,
+ int start, int nr_atoms,
+ rvec x[], rvec v[], const unsigned short cFREEZE[],
+ t_nrnb *nrnb);
+
// TODO: This doesn't seem to be used or implemented anywhere
void correct_ekin(FILE *log, int start, int end, rvec v[],
rvec vcm, real mass[], real tmass, tensor ekin);
diff --git a/src/gromacs/mdtypes/inputrec.cpp b/src/gromacs/mdtypes/inputrec.cpp
index 1afe02a840..596d8b5bf3 100644
--- a/src/gromacs/mdtypes/inputrec.cpp
+++ b/src/gromacs/mdtypes/inputrec.cpp
@@ -183,7 +183,8 @@ int pcouple_min_integration_steps(int epc)
case epcNO:
n = 0;
break;
- case etcBERENDSEN:
+ case epcBERENDSEN:
+ case epcCRESCALE:
case epcISOTROPIC:
n = nstmin_berendsen_pcouple;
break;
diff --git a/src/gromacs/mdtypes/md_enums.cpp b/src/gromacs/mdtypes/md_enums.cpp
index 3b03645e3f..2d8308ea19 100644
--- a/src/gromacs/mdtypes/md_enums.cpp
+++ b/src/gromacs/mdtypes/md_enums.cpp
@@ -108,7 +108,7 @@ const char *etcoupl_names[etcNR+1] = {
}; /* yes is alias for berendsen */
const char *epcoupl_names[epcNR+1] = {
- "No", "Berendsen", "Parrinello-Rahman", "Isotropic", "MTTK", nullptr
+ "No", "Berendsen", "Parrinello-Rahman", "Isotropic", "MTTK", "C-rescale", nullptr
}; /* isotropic is alias for berendsen */
const char *epcoupltype_names[epctNR+1] = {
diff --git a/src/gromacs/mdtypes/md_enums.h b/src/gromacs/mdtypes/md_enums.h
index f5cf68e68e..df0bb57d12 100644
--- a/src/gromacs/mdtypes/md_enums.h
+++ b/src/gromacs/mdtypes/md_enums.h
@@ -94,7 +94,7 @@ extern const char *etcoupl_names[etcNR+1];
* isotropic is an alias for berendsen
*/
enum {
- epcNO, epcBERENDSEN, epcPARRINELLORAHMAN, epcISOTROPIC, epcMTTK, epcNR
+ epcNO, epcBERENDSEN, epcPARRINELLORAHMAN, epcISOTROPIC, epcMTTK, epcCRESCALE, epcNR
};
//! String corresponding to pressure coupling algorithm
extern const char *epcoupl_names[epcNR+1];
EOF