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32.1460000 16.0730000 + 862 862 1 0.0000000 26.7880000 32.1460000 21.4310000 + 863 863 1 0.0000000 26.7880000 32.1460000 26.7880000 + 864 864 1 0.0000000 26.7880000 32.1460000 32.1460000 + diff --git a/examples/gjf/ff-argon.lmp b/examples/gjf/ff-argon.lmp new file mode 100644 index 0000000000..b6f7bc931a --- /dev/null +++ b/examples/gjf/ff-argon.lmp @@ -0,0 +1,20 @@ +############################# +#Atoms types - mass - charge# +############################# +#@ 1 atom types #!THIS LINE IS NECESSARY DON'T SPEND HOURS FINDING THAT OUT!# + +variable Ar equal 1 + +############# +#Atom Masses# +############# + +mass ${Ar} 39.903 + +########################### +#Pair Potentials - Tersoff# +########################### + +pair_style lj/cubic +pair_coeff * * 0.0102701 3.42 + diff --git a/examples/gjf/in.argon b/examples/gjf/in.argon new file mode 100644 index 0000000000..271882c665 --- /dev/null +++ b/examples/gjf/in.argon @@ -0,0 +1,162 @@ +###############################mm +# Atom style - charge/vdw/bonded# +################################# +atom_style full + +############################################## +#Units Metal : eV - ps - angstrom - bar# +# Real : kcal/mol - fs - angstrom - atm# +############################################## +units metal + +############ +#Run number# +############ +variable run_no equal 0 # is it a restart? +variable res_no equal ${run_no}-1 # restart file number + +####################################### +#Random Seeds and Domain Decomposition# +####################################### +variable iseed0 equal 2357 +variable iseed1 equal 26488 +variable iseed2 equal 10669 +processors * * * + +########### +#Data File# +########### +variable inpfile string argon.lmp +variable resfile string final_restart.${res_no} +variable ff_file string ff-argon.lmp + +########## +#Run Type# +########## +variable minimise equal 0 #Energy Minimization +variable md equal 1 #Plain MD + +############################### +#Molecular Dynamics Parameters# +############################### +variable run_no equal 0 # is it a restart? + +variable ens equal 9 # ensemble (0=nve, 1=nvt, 2=npt, 3=ber, 4=lang, 5=stoc, 6=vres, 7=stoch, 8=gjf) +variable ts equal 0.120 # simulation timestep (time units) +variable nequil equal 0 # number of equilibration steps +variable nsteps equal 200000 # number of MD steps +#variable nsteps equal 20 # number of MD steps + +variable temp_s equal 10 # starting temperature +variable temp_f equal 10 # final simulation temperature +variable trel equal 1 # thermostat relaxation time +variable tscale equal 1 # thermostat relaxation freq - vel rescaling only +variable deltat equal 1 # maximum temperature change - vel rescaling only + +variable npttype string iso # type of NPT (iso, aniso, tri, z...) +variable pres equal 1.01325 # pressure (NPT runs only) +variable prel equal 1.0 # barostat relaxation time + +neighbor 1 bin + +################### +#Output Parameters# +################### +variable ntraj equal 1000 # trajectory output frequency - all system +variable ntraj_s equal -100 # trajectory output frequency - solute only +variable nthermo equal 200 # thermodynamic data output frequency + +################################ +#Energy Minimization Parameters# +################################ +variable mtraj equal 1 # trajectory output frequency - all system +variable etol equal 1e-5 # % change in energy +variable ftol equal 1e-5 # max force threshold (force units) +variable maxiter equal 10000 # max # of iterations + +######################## +#3D Periodic Simulation# +######################## +boundary p p p + +############################# +#Reading the input structure# +############################# +if "${run_no} == 0" then "read_data ${inpfile}" else "read_restart ${resfile}" + +############# +#Force Field# +############# +include ${ff_file} + +###################### +#Thermodynamic Output# +###################### +variable str_basic string 'step time pe temp press' + +#MD ensemble (0=nve, 1=nvt, 2=npt, 3=ber, 4=lang, 5=stoc, 6=vres) +variable str_ens string ' ' +if "${ens} == 0" then "variable str_ens string 'etotal'" +if "${ens} == 2" then "variable str_ens string 'vol pxx pyy pzz cella cellb cellc cellakpha cellbeta cellgamma'" + +#Variable for a gulp friend output +if "${ens} >= 0" then "thermo_style custom time temp pe etotal press vol cpu" & + "thermo ${nthermo}" & + "thermo_modify flush yes" + +##################### +#Energy Minimization# +##################### +if "${minimise} <= 0 || ${run_no} > 0" then "jump SELF end_minimise" + print "Doing CG minimisation" + dump mdcd all dcd ${mtraj} min.dcd + dump_modify mdcd unwrap yes + min_style cg + min_modify line quadratic + minimize ${etol} ${ftol} ${maxiter} ${maxiter} + reset_timestep 0 + undump mdcd +label end_minimise + +################ +#Timestep in ps# +################ +timestep ${ts} + +############## +#Restart file# +############## +restart 100000 restart.1 restart.2 + +################### +#Trajectory output# +################### +#dump xyz all atom 1000 silicon.lammpstrj + +if "${ntraj} > 0" then & + "dump 1 all dcd ${ntraj} trajectory.${run_no}.dcd" & + "dump_modify 1 unwrap yes" + +fix mom all momentum 1 linear 1 1 1 + +############################################################### +#Ensembles (0=nve,1=nvt, 2=npt, 3=ber, 4=lang, 5=stoc, 6=vres)# +############################################################### +if "${md} > 0" then 'print "Setting up the ensembles"' & + 'if "${run_no} == 0" then "velocity all create ${temp_s} ${iseed0} mom yes dist gaussian"' & + 'if "${ens} == 0" then "fix nve all nve"' & + 'if "${ens} == 1" then "fix nvt all nvt temp ${temp_s} ${temp_f} ${trel} tchain 5"' & + 'if "${ens} == 2" then "fix npt all npt temp ${temp_s} ${temp_f} ${trel} ${npttype} ${pres} ${pres} ${prel} tchain 5 pchain 5 mtk yes"' & + 'if "${ens} == 3" then "fix nve all nve" "fix ber all temp/berendsen ${temp_s} ${temp_f} ${trel}"' & + 'if "${ens} == 4" then "fix nve all nve" "fix lang all langevin ${temp_s} ${temp_f} ${trel} ${iseed1} tally yes zero yes"' & + 'if "${ens} == 5" then "fix nve all nve" "fix stoch all temp/csvr ${temp_s} ${temp_f} ${trel} ${iseed1}"' & + 'if "${ens} == 6" then "fix nve all nve" "fix stoch all temp/csld ${temp_s} ${temp_f} ${trel} ${iseed1}"' & + 'if "${ens} == 7" then "fix nve all nve" "fix vres all temp/rescale ${tscale} ${temp_s} ${temp_f} ${tmin} ${tmax}"' & + 'if "${ens} == 8" then "fix nve all nve" "fix lang all langevin ${temp_s} ${temp_f} ${trel} ${iseed1} gjf yes"' & + 'if "${ens} == 9" then "fix nve all nve" "fix lang all langevin ${temp_s} ${temp_f} ${trel} ${iseed1} gjf yes halfstep yes"' + +if "${md} > 0" then "print 'Doing Molecular dynamics'" & + "run ${nsteps}" & + "write_restart final_restart.${run_no}" + + diff --git a/examples/gjf/out.argon b/examples/gjf/out.argon new file mode 100644 index 0000000000..8dda569157 --- /dev/null +++ b/examples/gjf/out.argon @@ -0,0 +1,249 @@ +LAMMPS (1 Feb 2019) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87) + using 1 OpenMP thread(s) per MPI task +Reading data file ... + orthogonal box = (0 0 0) to (32.146 32.146 32.146) + 1 by 2 by 2 MPI processor grid + reading atoms ... + 864 atoms +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 0 0 + special bond factors coul: 0 0 0 + 0 = max # of 1-2 neighbors + 0 = max # of 1-3 neighbors + 0 = max # of 1-4 neighbors + 1 = max # of special neighbors +Setting up the ensembles +WARNING: Careful, tally is untested (src/fix_langevin.cpp:145) +WARNING: Careful, tally is untested (src/fix_langevin.cpp:145) +WARNING: Careful, tally is untested (src/fix_langevin.cpp:145) +WARNING: Careful, tally is untested (src/fix_langevin.cpp:145) +Doing Molecular dynamics +Neighbor list info ... + update every 1 steps, delay 10 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 6.94072 + ghost atom cutoff = 6.94072 + binsize = 3.47036, bins = 10 10 10 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cubic, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d/newton + bin: standard +Setting up Verlet run ... + Unit style : metal + Current step : 0 + Time step : 0.12 +Per MPI rank memory allocation (min/avg/max) = 6.847 | 6.847 | 6.847 Mbytes +Time Temp PotEng TotEng Press Volume CPU + 0 10 -56.207655 -55.09214 33.340921 33218.561 0 + 24 10.156356 -55.092888 -53.959932 339.40964 33218.561 0.082175482 + 48 9.6121006 -55.07262 -54.000376 344.56765 33218.561 0.19529325 + 72 9.8187467 -55.16687 -54.071574 318.85979 33218.561 0.29643488 + 96 9.5421385 -55.151229 -54.086789 322.8842 33218.561 0.38801357 + 120 10.295035 -55.12919 -53.980763 332.00171 33218.561 0.47607262 + 144 10.331608 -55.09907 -53.946563 339.28896 33218.561 0.57389224 + 168 10.154698 -55.058246 -53.925475 349.03253 33218.561 0.65481471 + 192 9.858198 -55.127583 -54.027886 330.09298 33218.561 0.74437734 + 216 9.6658918 -55.10812 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3f2ec20db0..0db60c14cf 100644 --- a/src/fix_langevin.cpp +++ b/src/fix_langevin.cpp @@ -98,6 +98,7 @@ FixLangevin::FixLangevin(LAMMPS *lmp, int narg, char **arg) : oflag = 0; tallyflag = 0; zeroflag = 0; + hsflag = 0; int iarg = 7; while (iarg < narg) { @@ -138,6 +139,14 @@ FixLangevin::FixLangevin(LAMMPS *lmp, int narg, char **arg) : else if (strcmp(arg[iarg+1],"yes") == 0) zeroflag = 1; else error->all(FLERR,"Illegal fix langevin command"); iarg += 2; + } else if (strcmp(arg[iarg],"halfstep") == 0) { + if (iarg+2 > narg) error->all(FLERR,"Illegal fix langevin command"); + if (gjfflag == 0) error->all(FLERR,"GJF must be set"); + if (tallyflag == 0) error->warning(FLERR,"Careful, tally is untested"); + if (strcmp(arg[iarg+1],"no") == 0) hsflag = 0; + else if (strcmp(arg[iarg+1],"yes") == 0) hsflag = 1; + else error->all(FLERR,"Illegal fix langevin command"); + iarg += 2; } else error->all(FLERR,"Illegal fix langevin command"); } @@ -155,6 +164,8 @@ FixLangevin::FixLangevin(LAMMPS *lmp, int narg, char **arg) : flangevin = NULL; flangevin_allocated = 0; franprev = NULL; + wildcard = NULL; + lv = NULL; tforce = NULL; maxatom1 = maxatom2 = 0; @@ -163,6 +174,12 @@ FixLangevin::FixLangevin(LAMMPS *lmp, int narg, char **arg) : // no need to set peratom_flag, b/c data is for internal use only if (gjfflag) { + int mem = 6*atom->nmax*sizeof(double); + if (hsflag) mem += 3*atom->nmax*sizeof(double); + + comm->maxexchange_fix = MAX(comm->maxexchange_fix, 0); + comm->maxexchange_fix += MAX(1000, mem); + nvalues = 3; grow_arrays(atom->nmax); atom->add_callback(0); @@ -174,6 +191,14 @@ FixLangevin::FixLangevin(LAMMPS *lmp, int narg, char **arg) : franprev[i][0] = 0.0; franprev[i][1] = 0.0; franprev[i][2] = 0.0; + wildcard[i][0] = 0.0; + wildcard[i][1] = 0.0; + wildcard[i][2] = 0.0; + if (hsflag) { + lv[i][0] = 0.0; + lv[i][1] = 0.0; + lv[i][2] = 0.0; + } } } @@ -194,6 +219,8 @@ FixLangevin::~FixLangevin() if (gjfflag) { memory->destroy(franprev); + memory->destroy(wildcard); + if (hsflag) memory->destroy(lv); atom->delete_callback(id,0); } } @@ -203,6 +230,8 @@ FixLangevin::~FixLangevin() int FixLangevin::setmask() { int mask = 0; + //if (gjfflag) mask |= INITIAL_INTEGRATE; + if (gjfflag) mask |= POST_INTEGRATE; mask |= POST_FORCE; mask |= POST_FORCE_RESPA; mask |= END_OF_STEP; @@ -258,13 +287,11 @@ void FixLangevin::init() error->one(FLERR,"Fix langevin angmom requires extended particles"); } - // set force prefactors - if (!atom->rmass) { for (int i = 1; i <= atom->ntypes; i++) { gfactor1[i] = -atom->mass[i] / t_period / force->ftm2v; gfactor2[i] = sqrt(atom->mass[i]) * - sqrt(24.0*force->boltz/t_period/update->dt/force->mvv2e) / + sqrt(2.0*force->boltz/t_period/update->dt/force->mvv2e) / force->ftm2v; gfactor1[i] *= 1.0/ratio[i]; gfactor2[i] *= 1.0/sqrt(ratio[i]); @@ -277,7 +304,7 @@ void FixLangevin::init() if (strstr(update->integrate_style,"respa")) nlevels_respa = ((Respa *) update->integrate)->nlevels; - if (gjfflag) gjffac = 1.0/(1.0+update->dt/2.0/t_period); + if (gjfflag) gjffac = 1.0/sqrt(1.0+update->dt/2.0/t_period); } @@ -292,6 +319,94 @@ void FixLangevin::setup(int vflag) post_force_respa(vflag,nlevels_respa-1,0); ((Respa *) update->integrate)->copy_f_flevel(nlevels_respa-1); } + if (gjfflag && hsflag) { + + double dt = update->dt; + + // update v of atoms in group + + double **v = atom->v; + double *rmass = atom->rmass; + int *type = atom->type; + int nlocal = atom->nlocal; + if (igroup == atom->firstgroup) nlocal = atom->nfirst; + + double boltz = force->boltz; + double mvv2e = force->mvv2e; + double ftm2v = force->ftm2v; + + double gamma2; + + for (int i = 0; i < nlocal; i++) { + if (rmass) { + gamma2 = sqrt(rmass[i]) * sqrt(2.0*boltz/t_period/dt/mvv2e) / ftm2v; + gamma2 *= 1.0/sqrt(ratio[type[i]]) * tsqrt; + } else { + gamma2 = gfactor2[type[i]] * tsqrt; + } + + franprev[i][0] = gamma2*random->gaussian(); + franprev[i][1] = gamma2*random->gaussian(); + franprev[i][2] = gamma2*random->gaussian(); + wildcard[i][0] = v[i][0]; + wildcard[i][1] = v[i][1]; + wildcard[i][2] = v[i][2]; + } + } +} + +/* ---------------------------------------------------------------------- + allow for both per-type and per-atom mass +------------------------------------------------------------------------- */ + +void FixLangevin::post_integrate() +{ + double dtfm; + double dt = update->dt; + double dtf = 0.5 * dt * force->ftm2v; + + // update v of atoms in group + + double **x = atom->x; + double **v = atom->v; + double **f = atom->f; + double *rmass = atom->rmass; + double *mass = atom->mass; + int *type = atom->type; + int *mask = atom->mask; + int nlocal = atom->nlocal; + if (igroup == atom->firstgroup) nlocal = atom->nfirst; + + if (rmass) { + for (int i = 0; i < nlocal; i++) + if (mask[i] & groupbit) { + dtfm = dtf / rmass[i]; + x[i][0] += -dt * v[i][0]; + x[i][1] += -dt * v[i][1]; + x[i][2] += -dt * v[i][2]; + v[i][0] = gjffac * (wildcard[i][0] + dtfm * franprev[i][0] + dtfm * f[i][0]); + v[i][1] = gjffac * (wildcard[i][1] + dtfm * franprev[i][1] + dtfm * f[i][1]); + v[i][2] = gjffac * (wildcard[i][2] + dtfm * franprev[i][2] + dtfm * f[i][2]); + x[i][0] += gjffac * dt * v[i][0]; + x[i][1] += gjffac * dt * v[i][1]; + x[i][2] += gjffac * dt * v[i][2]; + } + + } else { + for (int i = 0; i < nlocal; i++) + if (mask[i] & groupbit) { + dtfm = dtf / mass[type[i]]; + x[i][0] += -dt * v[i][0]; + x[i][1] += -dt * v[i][1]; + x[i][2] += -dt * v[i][2]; + v[i][0] = gjffac * (wildcard[i][0] + dtfm * franprev[i][0] + dtfm * f[i][0]); + v[i][1] = gjffac * (wildcard[i][1] + dtfm * franprev[i][1] + dtfm * f[i][1]); + v[i][2] = gjffac * (wildcard[i][2] + dtfm * franprev[i][2] + dtfm * f[i][2]); + x[i][0] += gjffac * dt * v[i][0]; + x[i][1] += gjffac * dt * v[i][1]; + x[i][2] += gjffac * dt * v[i][2]; + } + } } /* ---------------------------------------------------------------------- */ @@ -477,9 +592,8 @@ void FixLangevin::post_force_templated() // sum random force over all atoms in group // subtract sum/count from each atom in group - double fdrag[3],fran[3],fsum[3],fsumall[3]; + double fdrag[3],fran[3],fsum[3],fsumall[3], rantemp[3]; bigint count; - double fswap; double boltz = force->boltz; double dt = update->dt; @@ -513,7 +627,7 @@ void FixLangevin::post_force_templated() if (Tp_TSTYLEATOM) tsqrt = sqrt(tforce[i]); if (Tp_RMASS) { gamma1 = -rmass[i] / t_period / ftm2v; - gamma2 = sqrt(rmass[i]) * sqrt(24.0*boltz/t_period/dt/mvv2e) / ftm2v; + gamma2 = sqrt(rmass[i]) * sqrt(2.0*boltz/t_period/dt/mvv2e) / ftm2v; gamma1 *= 1.0/ratio[type[i]]; gamma2 *= 1.0/sqrt(ratio[type[i]]) * tsqrt; } else { @@ -521,9 +635,9 @@ void FixLangevin::post_force_templated() gamma2 = gfactor2[type[i]] * tsqrt; } - fran[0] = gamma2*(random->uniform()-0.5); - fran[1] = gamma2*(random->uniform()-0.5); - fran[2] = gamma2*(random->uniform()-0.5); + fran[0] = gamma2*random->gaussian(); + fran[1] = gamma2*random->gaussian(); + fran[2] = gamma2*random->gaussian(); if (Tp_BIAS) { temperature->remove_bias(i,v[i]); @@ -541,25 +655,20 @@ void FixLangevin::post_force_templated() } if (Tp_GJF) { - fswap = 0.5*(fran[0]+franprev[i][0]); - franprev[i][0] = fran[0]; - fran[0] = fswap; - fswap = 0.5*(fran[1]+franprev[i][1]); - franprev[i][1] = fran[1]; - fran[1] = fswap; - fswap = 0.5*(fran[2]+franprev[i][2]); - franprev[i][2] = fran[2]; - fran[2] = fswap; + wildcard[i][0] = f[i][0]; + wildcard[i][1] = f[i][1]; + wildcard[i][2] = f[i][2]; - fdrag[0] *= gjffac; - fdrag[1] *= gjffac; - fdrag[2] *= gjffac; - fran[0] *= gjffac; - fran[1] *= gjffac; - fran[2] *= gjffac; - f[i][0] *= gjffac; - f[i][1] *= gjffac; - f[i][2] *= gjffac; + rantemp[0] = fran[0]; + rantemp[1] = fran[1]; + rantemp[2] = fran[2]; + fran[0] = franprev[i][0]; + fran[1] = franprev[i][1]; + fran[2] = franprev[i][2]; + + fdrag[0] *= -2*t_period*(2*gjffac-1/gjffac-1)/dt; + fdrag[1] *= -2*t_period*(2*gjffac-1/gjffac-1)/dt; + fdrag[2] *= -2*t_period*(2*gjffac-1/gjffac-1)/dt; } f[i][0] += fdrag[0] + fran[0]; @@ -567,6 +676,11 @@ void FixLangevin::post_force_templated() f[i][2] += fdrag[2] + fran[2]; if (Tp_TALLY) { + if (Tp_GJF){ + fdrag[0] = gamma1*gjffac*v[i][0]; + fdrag[1] = gamma1*gjffac*v[i][1]; + fdrag[2] = gamma1*gjffac*v[i][2]; + } flangevin[i][0] = fdrag[0] + fran[0]; flangevin[i][1] = fdrag[1] + fran[1]; flangevin[i][2] = fdrag[2] + fran[2]; @@ -577,6 +691,19 @@ void FixLangevin::post_force_templated() fsum[1] += fran[1]; fsum[2] += fran[2]; } + + if (Tp_GJF) + { + franprev[i][0] = rantemp[0]; + franprev[i][1] = rantemp[1]; + franprev[i][2] = rantemp[2]; + + if (hsflag){ + lv[i][0] = v[i][0]; + lv[i][1] = v[i][1]; + lv[i][2] = v[i][2]; + } + } } } @@ -641,9 +768,9 @@ void FixLangevin::compute_target() input->variable->compute_atom(tvar,igroup,tforce,1,0); for (int i = 0; i < nlocal; i++) if (mask[i] & groupbit) - if (tforce[i] < 0.0) - error->one(FLERR, - "Fix langevin variable returned negative temperature"); + if (tforce[i] < 0.0) + error->one(FLERR, + "Fix langevin variable returned negative temperature"); } modify->addstep_compute(update->ntimestep + 1); } @@ -756,20 +883,41 @@ void FixLangevin::angmom_thermostat() void FixLangevin::end_of_step() { - if (!tallyflag) return; + if (!tallyflag && !gjfflag) return; double **v = atom->v; + double **f = atom->f; int *mask = atom->mask; int nlocal = atom->nlocal; energy_onestep = 0.0; - for (int i = 0; i < nlocal; i++) - if (mask[i] & groupbit) - energy_onestep += flangevin[i][0]*v[i][0] + flangevin[i][1]*v[i][1] + - flangevin[i][2]*v[i][2]; - - energy += energy_onestep*update->dt; + if (mask[i] & groupbit) { + if (gjfflag){ + f[i][0] = wildcard[i][0]; + f[i][1] = wildcard[i][1]; + f[i][2] = wildcard[i][2]; + wildcard[i][0] = v[i][0]; + wildcard[i][1] = v[i][1]; + wildcard[i][2] = v[i][2]; + if (hsflag){ + v[i][0] = lv[i][0]; + v[i][1] = lv[i][1]; + v[i][2] = lv[i][2]; + } + } + if (tallyflag && hsflag){ + energy_onestep += gjffac*(flangevin[i][0] * lv[i][0] + + flangevin[i][1] * lv[i][1] + flangevin[i][2] * lv[i][2]); + } + else if (tallyflag){ + energy_onestep += flangevin[i][0] * v[i][0] + flangevin[i][1] * v[i][1] + + flangevin[i][2] * v[i][2]; + } + } + if (tallyflag) { + energy += energy_onestep * update->dt; + } } /* ---------------------------------------------------------------------- */ @@ -869,7 +1017,8 @@ void *FixLangevin::extract(const char *str, int &dim) double FixLangevin::memory_usage() { double bytes = 0.0; - if (gjfflag) bytes += atom->nmax*3 * sizeof(double); + if (gjfflag) bytes += atom->nmax*3*2 * sizeof(double); + if (gjfflag) if (hsflag) bytes += atom->nmax*3 * sizeof(double); if (tallyflag) bytes += atom->nmax*3 * sizeof(double); if (tforce) bytes += atom->nmax * sizeof(double); return bytes; @@ -882,6 +1031,8 @@ double FixLangevin::memory_usage() void FixLangevin::grow_arrays(int nmax) { memory->grow(franprev,nmax,3,"fix_langevin:franprev"); + memory->grow(wildcard,nmax,3,"fix_langevin:wildcard"); + if (hsflag) memory->grow(lv,nmax,3,"fix_langevin:lv"); } /* ---------------------------------------------------------------------- @@ -890,8 +1041,17 @@ void FixLangevin::grow_arrays(int nmax) void FixLangevin::copy_arrays(int i, int j, int /*delflag*/) { - for (int m = 0; m < nvalues; m++) - franprev[j][m] = franprev[i][m]; + franprev[j][0] = franprev[i][0]; + franprev[j][1] = franprev[i][1]; + franprev[j][2] = franprev[i][2]; + wildcard[j][0] = wildcard[i][0]; + wildcard[j][1] = wildcard[i][1]; + wildcard[j][2] = wildcard[i][2]; + if (hsflag) { + lv[j][0] = lv[i][0]; + lv[j][1] = lv[i][1]; + lv[j][2] = lv[i][2]; + } } /* ---------------------------------------------------------------------- @@ -900,8 +1060,19 @@ void FixLangevin::copy_arrays(int i, int j, int /*delflag*/) int FixLangevin::pack_exchange(int i, double *buf) { - for (int m = 0; m < nvalues; m++) buf[m] = franprev[i][m]; - return nvalues; + int n = 0; + buf[n++] = franprev[i][0]; + buf[n++] = franprev[i][1]; + buf[n++] = franprev[i][2]; + buf[n++] = wildcard[i][0]; + buf[n++] = wildcard[i][1]; + buf[n++] = wildcard[i][2]; + if (hsflag){ + buf[n++] = lv[i][0]; + buf[n++] = lv[i][1]; + buf[n++] = lv[i][2]; + } + return n; } /* ---------------------------------------------------------------------- @@ -910,6 +1081,17 @@ int FixLangevin::pack_exchange(int i, double *buf) int FixLangevin::unpack_exchange(int nlocal, double *buf) { - for (int m = 0; m < nvalues; m++) franprev[nlocal][m] = buf[m]; - return nvalues; + int n = 0; + franprev[nlocal][0] = buf[n++]; + franprev[nlocal][1] = buf[n++]; + franprev[nlocal][2] = buf[n++]; + wildcard[nlocal][0] = buf[n++]; + wildcard[nlocal][1] = buf[n++]; + wildcard[nlocal][2] = buf[n++]; + if (hsflag){ + lv[nlocal][0] = buf[n++]; + lv[nlocal][1] = buf[n++]; + lv[nlocal][2] = buf[n++]; + } + return n; } diff --git a/src/fix_langevin.h b/src/fix_langevin.h index 4b5570ac2e..461d4e5140 100644 --- a/src/fix_langevin.h +++ b/src/fix_langevin.h @@ -31,6 +31,8 @@ class FixLangevin : public Fix { int setmask(); void init(); void setup(int); + //virtual void initial_integrate(int); + virtual void post_integrate(); virtual void post_force(int); void post_force_respa(int, int, int); virtual void end_of_step(); @@ -46,7 +48,7 @@ class FixLangevin : public Fix { int unpack_exchange(int, double *); protected: - int gjfflag,oflag,tallyflag,zeroflag,tbiasflag; + int gjfflag,oflag,tallyflag,zeroflag,tbiasflag,hsflag; int flangevin_allocated; double ascale; double t_start,t_stop,t_period,t_target; @@ -63,6 +65,9 @@ class FixLangevin : public Fix { double **flangevin; double *tforce; double **franprev; + double **lv; //lucas velocity or half-step velocity + double **wildcard; + int nvalues; char *id_temp;