diff --git a/doc/src/Errors_messages.txt b/doc/src/Errors_messages.txt index c131b10ec6..33593d4d53 100644 --- a/doc/src/Errors_messages.txt +++ b/doc/src/Errors_messages.txt @@ -4791,6 +4791,22 @@ Self-explanatory. :dd This fix option cannot be used with point particles. :dd +{Fix langevin gjf and respa are not compatible} :dt + +Self-explanatory. :dd + +{Fix langevin gjf cannot have period equal to dt/2} :dt + +If the period is equal to dt/2 then division by zero will happen. :dd + +{Fix langevin gjf should come before fix nve} :dt + +Self-explanatory. :dd + +{Fix langevin gjf with tbias is not yet implemented with kokkos} :dt + +This option is not yet available. :dd + {Fix langevin omega is not yet implemented with kokkos} :dt This option is not yet available. :dd diff --git a/doc/src/Errors_warnings.txt b/doc/src/Errors_warnings.txt index 9f346ba8c1..fbd857f162 100644 --- a/doc/src/Errors_warnings.txt +++ b/doc/src/Errors_warnings.txt @@ -248,6 +248,10 @@ included one or more of the following: kspace, triclinic, a hybrid pair style, an eam pair style, or no "single" function for the pair style. :dd +{Fix langevin gjf using random gaussians is not implemented with kokkos} :dt + +This will most likely cause errors in kinetic fluctuations. + {Fix property/atom mol or charge w/out ghost communication} :dt A model typically needs these properties defined for ghost atoms. :dd diff --git a/doc/src/fix_langevin.txt b/doc/src/fix_langevin.txt index 861eed4a6f..07d8b274aa 100644 --- a/doc/src/fix_langevin.txt +++ b/doc/src/fix_langevin.txt @@ -24,9 +24,10 @@ keyword = {angmom} or {omega} or {scale} or {tally} or {zero} :l {angmom} value = {no} or factor {no} = do not thermostat rotational degrees of freedom via the angular momentum factor = do thermostat rotational degrees of freedom via the angular momentum and apply numeric scale factor as discussed below - {gjf} value = {no} or {yes} + {gjf} value = {no} or {vfull} or {vhalf} {no} = use standard formulation - {yes} = use Gronbech-Jensen/Farago formulation + {vfull} = use Gronbech-Jensen/Farago formulation + {vhalf} = use 2GJ formulation {omega} value = {no} or {yes} {no} = do not thermostat rotational degrees of freedom via the angular velocity {yes} = do thermostat rotational degrees of freedom via the angular velocity @@ -217,6 +218,10 @@ the particles. As described below, this energy can then be printed out or added to the potential energy of the system to monitor energy conservation. +NOTE: this accumulated energy does NOT include kinetic energy removed +by the {zero} flag. LAMMPS will print a warning when both options are +active. + The keyword {zero} can be used to eliminate drift due to the thermostat. Because the random forces on different atoms are independent, they do not sum exactly to zero. As a result, this fix @@ -232,29 +237,24 @@ The keyword {gjf} can be used to run the "Gronbech-Jensen/Farago described in the papers cited below, the purpose of this method is to enable longer timesteps to be used (up to the numerical stability limit of the integrator), while still producing the correct Boltzmann -distribution of atom positions. It is implemented within LAMMPS, by -changing how the random force is applied so that it is composed of -the average of two random forces representing half-contributions from -the previous and current time intervals. +distribution of atom positions. -In common with all methods based on Verlet integration, the -discretized velocities generated by this method in conjunction with -velocity-Verlet time integration are not exactly conjugate to the -positions. As a result the temperature (computed from the discretized -velocities) will be systematically lower than the target temperature, -by a small amount which grows with the timestep. Nonetheless, the -distribution of atom positions will still be consistent with the +The current implementation provides the user with the option to output +the velocity in one of two forms: {vfull} or {vhalf}, which replaces +the outdated option {yes}. The {gjf} option {vfull} outputs the on-site +velocity given in "Gronbech-Jensen/Farago"_#Gronbech-Jensen; this velocity +is shown to be systematically lower than the target temperature by a small +amount, which grows quadratically with the timestep. +The {gjf} option {vhalf} outputs the 2GJ half-step velocity given in +"Gronbech Jensen/Gronbech-Jensen"_#2Gronbech-Jensen; this velocity is shown +to not have any linear statistical errors for any stable time step. +An overview of statistically correct Boltzmann and Maxwell-Boltzmann +sampling of true on-site and true half-step velocities is given in +"Gronbech-Jensen_#1Gronbech-Jensen. +Regardless of the choice of output velocity, the sampling of the configurational +distribution of atom positions is the same, and linearly consistent with the target temperature. -As an example of using the {gjf} keyword, for molecules containing C-H -bonds, configurational properties generated with dt = 2.5 fs and tdamp -= 100 fs are indistinguishable from dt = 0.5 fs. Because the velocity -distribution systematically decreases with increasing timestep, the -method should not be used to generate properties that depend on the -velocity distribution, such as the velocity auto-correlation function -(VACF). In this example, the velocity distribution at dt = 2.5fs -generates an average temperature of 220 K, instead of 300 K. - :line Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are @@ -312,7 +312,10 @@ This fix can ramp its target temperature over multiple runs, using the This fix is not invoked during "energy minimization"_minimize.html. -[Restrictions:] none +[Restrictions:] + +For {gjf} do not choose damp=dt/2. {gjf} is not compatible +with run_style respa. [Related commands:] @@ -335,5 +338,10 @@ types, tally = no, zero = no, gjf = no. :link(Gronbech-Jensen) [(Gronbech-Jensen)] Gronbech-Jensen and Farago, Mol Phys, 111, 983 -(2013); Gronbech-Jensen, Hayre, and Farago, Comp Phys Comm, -185, 524 (2014) +(2013); Gronbech-Jensen, Hayre, and Farago, Comp Phys Comm, 185, 524 (2014) + +:link(2Gronbech-Jensen) +[(Gronbech-Jensen)] Gronbech Jensen and Gronbech-Jensen, Mol Phys, 117, 2511 (2019) + +:link(1Gronbech-Jensen) +[(Gronbech-Jensen)] Gronbech-Jensen, Mol Phys (2019); https://doi.org/10.1080/00268976.2019.1662506 diff --git a/doc/utils/sphinx-config/false_positives.txt b/doc/utils/sphinx-config/false_positives.txt index fd4612bf78..1f6e544ddb 100644 --- a/doc/utils/sphinx-config/false_positives.txt +++ b/doc/utils/sphinx-config/false_positives.txt @@ -2272,6 +2272,7 @@ qoffload qopenmp qoverride qtb +quadratically quadrupolar Quant quartic diff --git a/examples/gjf/README.md b/examples/gjf/README.md new file mode 100644 index 0000000000..e6886cb2dd --- /dev/null +++ b/examples/gjf/README.md @@ -0,0 +1,13 @@ +# LAMMPS GJF-2GJ THERMOSTAT EXAMPLE + +## GJF-2GJ THERMOSTAT + +This directory contains the ingredients to run an NVT simulation using the GJF-2GJ thermostat. + +Example: +``` +NP=4 #number of processors +mpirun -np $NP lmp_mpi -in.gjf.vhalf +``` + +## Required LAMMPS packages: MOLECULE package diff --git a/examples/gjf/argon.lmp b/examples/gjf/argon.lmp new file mode 100644 index 0000000000..00214b4c54 --- /dev/null +++ b/examples/gjf/argon.lmp @@ -0,0 +1,886 @@ +LAMMPS description + + 864 atoms + 0 bonds + 0 angles + 0 dihedrals + 0 impropers + + 1 atom types + 0 bond types + 0 angle types + 0 dihedral types + 0 improper types + + + 0.0000000 32.146000 xlo xhi + 0.0000000 32.146000 ylo yhi + 0.0000000 32.146000 zlo zhi + + Atoms + + 1 1 1 0.0000000 0.0000000 2.6790000 2.6790000 + 2 2 1 0.0000000 0.0000000 2.6790000 8.0360000 + 3 3 1 0.0000000 0.0000000 2.6790000 13.3940000 + 4 4 1 0.0000000 0.0000000 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855 855 1 0.0000000 26.7880000 26.7880000 16.0730000 + 856 856 1 0.0000000 26.7880000 26.7880000 21.4310000 + 857 857 1 0.0000000 26.7880000 26.7880000 26.7880000 + 858 858 1 0.0000000 26.7880000 26.7880000 32.1460000 + 859 859 1 0.0000000 26.7880000 32.1460000 5.3580000 + 860 860 1 0.0000000 26.7880000 32.1460000 10.7150000 + 861 861 1 0.0000000 26.7880000 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.gjf.vfull b/examples/gjf/in.gjf.vfull new file mode 100644 index 0000000000..19420e22ca --- /dev/null +++ b/examples/gjf/in.gjf.vfull @@ -0,0 +1,23 @@ +# GJF-2GJ thermostat + +units metal +atom_style full + +boundary p p p +read_data argon.lmp + +include ff-argon.lmp + +velocity all create 10 2357 mom yes dist gaussian + +neighbor 1 bin + +timestep 0.1 + +fix nve all nve +fix lang all langevin 10 10 1 26488 gjf vfull + +thermo 200 +run 50000 + + diff --git a/examples/gjf/in.gjf.vhalf b/examples/gjf/in.gjf.vhalf new file mode 100644 index 0000000000..74e2089595 --- /dev/null +++ b/examples/gjf/in.gjf.vhalf @@ -0,0 +1,23 @@ +# GJF-2GJ thermostat + +units metal +atom_style full + +boundary p p p +read_data argon.lmp + +include ff-argon.lmp + +velocity all create 10 2357 mom yes dist gaussian + +neighbor 1 bin + +timestep 0.1 + +fix nve all nve +fix lang all langevin 10 10 1 26488 gjf vhalf + +thermo 200 +run 50000 + + diff --git a/src/KOKKOS/fix_langevin_kokkos.cpp b/src/KOKKOS/fix_langevin_kokkos.cpp index 651f790a25..426bcb49e3 100644 --- a/src/KOKKOS/fix_langevin_kokkos.cpp +++ b/src/KOKKOS/fix_langevin_kokkos.cpp @@ -61,7 +61,6 @@ FixLangevinKokkos::FixLangevinKokkos(LAMMPS *lmp, int narg, char **a k_ratio.template modify(); if(gjfflag){ - nvalues = 3; grow_arrays(atomKK->nmax); atom->add_callback(0); // initialize franprev to zero @@ -69,8 +68,12 @@ FixLangevinKokkos::FixLangevinKokkos(LAMMPS *lmp, int narg, char **a franprev[i][0] = 0.0; franprev[i][1] = 0.0; franprev[i][2] = 0.0; + lv[i][0] = 0.0; + lv[i][1] = 0.0; + lv[i][2] = 0.0; } k_franprev.template modify(); + k_lv.template modify(); } if(zeroflag){ k_fsumall = tdual_double_1d_3n("langevin:fsumall"); @@ -94,6 +97,7 @@ FixLangevinKokkos::~FixLangevinKokkos() memoryKK->destroy_kokkos(k_ratio,ratio); memoryKK->destroy_kokkos(k_flangevin,flangevin); if(gjfflag) memoryKK->destroy_kokkos(k_franprev,franprev); + if(gjfflag) memoryKK->destroy_kokkos(k_lv,lv); memoryKK->destroy_kokkos(k_tforce,tforce); } @@ -107,6 +111,10 @@ void FixLangevinKokkos::init() error->all(FLERR,"Fix langevin omega is not yet implemented with kokkos"); if(ascale) error->all(FLERR,"Fix langevin angmom is not yet implemented with kokkos"); + if(gjfflag && tbiasflag) + error->all(FLERR,"Fix langevin gjf + tbias is not yet implemented with kokkos"); + if(gjfflag && tbiasflag) + error->warning(FLERR,"Fix langevin gjf + kokkos is not implemented with random gaussians"); // prefactors are modified in the init k_gfactor1.template modify(); @@ -121,6 +129,40 @@ void FixLangevinKokkos::grow_arrays(int nmax) memoryKK->grow_kokkos(k_franprev,franprev,nmax,3,"langevin:franprev"); d_franprev = k_franprev.template view(); h_franprev = k_franprev.template view(); + memoryKK->grow_kokkos(k_lv,lv,nmax,3,"langevin:lv"); + d_lv = k_lv.template view(); + h_lv = k_lv.template view(); +} + +/* ---------------------------------------------------------------------- */ + +template +void FixLangevinKokkos::initial_integrate(int vflag) +{ + atomKK->sync(execution_space,datamask_read); + atomKK->modified(execution_space,datamask_modify); + + v = atomKK->k_v.view(); + f = atomKK->k_f.view(); + int nlocal = atomKK->nlocal; + if (igroup == atomKK->firstgroup) nlocal = atomKK->nfirst; + + FixLangevinKokkosInitialIntegrateFunctor functor(this); + Kokkos::parallel_for(nlocal,functor); +} + +template +KOKKOS_INLINE_FUNCTION +void FixLangevinKokkos::initial_integrate_item(int i) const +{ + if (mask[i] & groupbit) { + f(i,0) /= gjfa; + f(i,1) /= gjfa; + f(i,2) /= gjfa; + v(i,0) = d_lv(i,0); + v(i,1) = d_lv(i,1); + v(i,2) = d_lv(i,2); + } } /* ---------------------------------------------------------------------- */ @@ -140,6 +182,7 @@ void FixLangevinKokkos::post_force(int vflag) k_gfactor2.template sync(); k_ratio.template sync(); if(gjfflag) k_franprev.template sync(); + if(gjfflag) k_lv.template sync(); boltz = force->boltz; dt = update->dt; @@ -177,7 +220,7 @@ void FixLangevinKokkos::post_force(int vflag) atomKK->sync(temperature->execution_space,temperature->datamask_read); temperature->compute_scalar(); temperature->remove_bias_all(); // modifies velocities - // if temeprature compute is kokkosized host-devcie comm won't be needed + // if temeprature compute is kokkosized host-device comm won't be needed atomKK->modified(temperature->execution_space,temperature->datamask_modify); atomKK->sync(execution_space,temperature->datamask_modify); } @@ -481,6 +524,7 @@ void FixLangevinKokkos::post_force(int vflag) // set modify flags for the views modified in post_force functor if (gjfflag) k_franprev.template modify(); + if (gjfflag) k_lv.template modify(); if (tallyflag) k_flangevin.template modify(); // set total force to zero @@ -550,6 +594,10 @@ FSUM FixLangevinKokkos::post_force_item(int i) const } if (Tp_GJF) { + d_lv(i,0) = gjfsib*v(i,0); + d_lv(i,1) = gjfsib*v(i,1); + d_lv(i,2) = gjfsib*v(i,2); + fswap = 0.5*(fran[0]+d_franprev(i,0)); d_franprev(i,0) = fran[0]; fran[0] = fswap; @@ -560,15 +608,15 @@ FSUM FixLangevinKokkos::post_force_item(int i) const d_franprev(i,2) = fran[2]; fran[2] = fswap; - 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; + fdrag[0] *= gjfa; + fdrag[1] *= gjfa; + fdrag[2] *= gjfa; + fran[0] *= gjfa; + fran[1] *= gjfa; + fran[2] *= gjfa; + f(i,0) *= gjfa; + f(i,1) *= gjfa; + f(i,2) *= gjfa; } f(i,0) += fdrag[0] + fran[0]; @@ -576,6 +624,17 @@ FSUM FixLangevinKokkos::post_force_item(int i) const f(i,2) += fdrag[2] + fran[2]; if (Tp_TALLY) { + if (Tp_GJF){ + fdrag[0] = gamma1*d_lv(i,0)/gjfsib/gjfsib; + fdrag[1] = gamma1*d_lv(i,1)/gjfsib/gjfsib; + fdrag[2] = gamma1*d_lv(i,2)/gjfsib/gjfsib; + fswap = (2*fran[0]/gjfa - d_franprev(i,0))/gjfsib; + fran[0] = fswap; + fswap = (2*fran[1]/gjfa - d_franprev(i,1))/gjfsib; + fran[1] = fswap; + fswap = (2*fran[2]/gjfa - d_franprev(i,2))/gjfsib; + fran[2] = fswap; + } d_flangevin(i,0) = fdrag[0] + fran[0]; d_flangevin(i,1) = fdrag[1] + fran[1]; d_flangevin(i,2) = fdrag[2] + fran[2]; @@ -719,9 +778,10 @@ double FixLangevinKokkos::compute_energy_item(int i) const template void FixLangevinKokkos::end_of_step() { - if (!tallyflag) return; + if (!tallyflag && !gjfflag) return; v = atomKK->k_v.template view(); + f = atomKK->k_f.template view(); mask = atomKK->k_mask.template view(); atomKK->sync(execution_space,V_MASK | MASK_MASK); @@ -733,9 +793,81 @@ void FixLangevinKokkos::end_of_step() FixLangevinKokkosTallyEnergyFunctor tally_functor(this); Kokkos::parallel_reduce(nlocal,tally_functor,energy_onestep); + if (gjfflag){ + if (rmass.data()) { + FixLangevinKokkosEndOfStepFunctor functor(this); + Kokkos::parallel_for(nlocal,functor); + } else { + mass = atomKK->k_mass.view(); + FixLangevinKokkosEndOfStepFunctor functor(this); + Kokkos::parallel_for(nlocal,functor); + } + } + energy += energy_onestep*update->dt; } +template +KOKKOS_INLINE_FUNCTION +void FixLangevinKokkos::end_of_step_item(int i) const { + double tmp[3]; + if (mask[i] & groupbit) { + const double dtfm = force->ftm2v * 0.5 * dt / mass[type[i]]; + tmp[0] = v(i,0); + tmp[1] = v(i,1); + tmp[2] = v(i,2); + if (!osflag){ + v(i,0) = d_lv(i,0); + v(i,1) = d_lv(i,1); + v(i,2) = d_lv(i,2); + } else { + v(i,0) = 0.5 * gjfsib * gjfsib * (v(i,0) + dtfm * f(i,0) / gjfa) + + dtfm * 0.5 * (gjfsib * d_flangevin(i,0) - d_franprev(i,0)) + + (gjfsib * gjfa * 0.5 + dt * 0.25 / t_period / gjfsib) * d_lv(i,0); + v(i,1) = 0.5 * gjfsib * gjfsib * (v(i,1) + dtfm * f(i,1) / gjfa) + + dtfm * 0.5 * (gjfsib * d_flangevin(i,0) - d_franprev(i,1)) + + (gjfsib * gjfa * 0.5 + dt * 0.25 / t_period / gjfsib) * d_lv(i,1); + v(i,2) = 0.5 * gjfsib * gjfsib * (v(i,2) + dtfm * f(i,2) / gjfa) + + dtfm * 0.5 * (gjfsib * d_flangevin(i,0) - d_franprev(i,2)) + + (gjfsib * gjfa * 0.5 + dt * 0.25 / t_period / gjfsib) * d_lv(i,2); + } + d_lv(i,0) = tmp[0]; + d_lv(i,1) = tmp[1]; + d_lv(i,2) = tmp[2]; + } +} + +template +KOKKOS_INLINE_FUNCTION +void FixLangevinKokkos::end_of_step_rmass_item(int i) const +{ + double tmp[3]; + if (mask[i] & groupbit) { + const double dtfm = force->ftm2v * 0.5 * dt / rmass[i]; + tmp[0] = v(i,0); + tmp[1] = v(i,1); + tmp[2] = v(i,2); + if (!osflag){ + v(i,0) = d_lv(i,0); + v(i,1) = d_lv(i,1); + v(i,2) = d_lv(i,2); + } else { + v(i,0) = 0.5 * gjfsib * gjfsib * (v(i,0) + dtfm * f(i,0) / gjfa) + + dtfm * 0.5 * (gjfsib * d_flangevin(i,0) - d_franprev(i,0)) + + (gjfsib * gjfa * 0.5 + dt * 0.25 / t_period / gjfsib) * d_lv(i,0); + v(i,1) = 0.5 * gjfsib * gjfsib * (v(i,1) + dtfm * f(i,1) / gjfa) + + dtfm * 0.5 * (gjfsib * d_flangevin(i,1) - d_franprev(i,1)) + + (gjfsib * gjfa * 0.5 + dt * 0.25 / t_period / gjfsib) * d_lv(i,1); + v(i,2) = 0.5 * gjfsib * gjfsib * (v(i,2) + dtfm * f(i,2) / gjfa) + + dtfm * 0.5 * (gjfsib * d_flangevin(i,2) - d_franprev(i,2)) + + (gjfsib * gjfa * 0.5 + dt * 0.25 / t_period / gjfsib) * d_lv(i,2); + } + d_lv(i,0) = tmp[0]; + d_lv(i,1) = tmp[1]; + d_lv(i,2) = tmp[2]; + } +} + /* ---------------------------------------------------------------------- copy values within local atom-based array ------------------------------------------------------------------------- */ @@ -743,10 +875,15 @@ void FixLangevinKokkos::end_of_step() template void FixLangevinKokkos::copy_arrays(int i, int j, int delflag) { - for (int m = 0; m < nvalues; m++) - h_franprev(j,m) = h_franprev(i,m); + h_franprev(j,0) = h_franprev(i,0); + h_franprev(j,1) = h_franprev(i,1); + h_franprev(j,2) = h_franprev(i,2); + h_lv(j,0) = h_lv(i,0); + h_lv(j,1) = h_lv(i,1); + h_lv(j,2) = h_lv(i,2); k_franprev.template modify(); + k_lv.template modify(); } @@ -765,6 +902,7 @@ void FixLangevinKokkos::cleanup_copy() tforce = NULL; gjfflag = 0; franprev = NULL; + lv = NULL; id = style = NULL; vatom = NULL; } diff --git a/src/KOKKOS/fix_langevin_kokkos.h b/src/KOKKOS/fix_langevin_kokkos.h index 140fea81d6..a6d467dfd7 100644 --- a/src/KOKKOS/fix_langevin_kokkos.h +++ b/src/KOKKOS/fix_langevin_kokkos.h @@ -56,6 +56,9 @@ namespace LAMMPS_NS { template class FixLangevinKokkos; + template + class FixLangevinKokkosInitialIntegrateFunctor; + template class FixLangevinKokkosPostForceFunctor; @@ -72,6 +75,7 @@ namespace LAMMPS_NS { void cleanup_copy(); void init(); + void initial_integrate(int); void post_force(int); void reset_dt(); void grow_arrays(int); @@ -79,6 +83,12 @@ namespace LAMMPS_NS { double compute_scalar(); void end_of_step(); + KOKKOS_INLINE_FUNCTION + void initial_integrate_item(int) const; + + KOKKOS_INLINE_FUNCTION + void initial_integrate_rmass_item(int) const; + template KOKKOS_INLINE_FUNCTION @@ -90,14 +100,25 @@ namespace LAMMPS_NS { KOKKOS_INLINE_FUNCTION double compute_energy_item(int) const; + KOKKOS_INLINE_FUNCTION + void end_of_step_item(int) const; + + KOKKOS_INLINE_FUNCTION + void end_of_step_rmass_item(int) const; + private: class CommKokkos *commKK; typename ArrayTypes::t_float_1d rmass; + typename ArrayTypes::t_float_1d mass; typename ArrayTypes::tdual_double_2d k_franprev; typename ArrayTypes::t_double_2d d_franprev; HAT::t_double_2d h_franprev; + typename ArrayTypes::tdual_double_2d k_lv; + typename ArrayTypes::t_double_2d d_lv; + HAT::t_double_2d h_lv; + typename ArrayTypes::tdual_double_2d k_flangevin; typename ArrayTypes::t_double_2d d_flangevin; HAT::t_double_2d h_flangevin; @@ -130,6 +151,21 @@ namespace LAMMPS_NS { }; + template + struct FixLangevinKokkosInitialIntegrateFunctor { + typedef DeviceType device_type ; + FixLangevinKokkos c; + + FixLangevinKokkosInitialIntegrateFunctor(FixLangevinKokkos* c_ptr): + c(*c_ptr) {c.cleanup_copy();}; + + KOKKOS_INLINE_FUNCTION + void operator()(const int i) const { + c.initial_integrate_item(i); + } + }; + + template struct FixLangevinKokkosPostForceFunctor { @@ -207,6 +243,21 @@ namespace LAMMPS_NS { update += source; } }; + + template + struct FixLangevinKokkosEndOfStepFunctor { + typedef DeviceType device_type ; + FixLangevinKokkos c; + + FixLangevinKokkosEndOfStepFunctor(FixLangevinKokkos* c_ptr): + c(*c_ptr) {c.cleanup_copy();} + + KOKKOS_INLINE_FUNCTION + void operator()(const int i) const { + if (RMass) c.end_of_step_rmass_item(i); + else c.end_of_step_item(i); + } + }; } #endif @@ -231,4 +282,12 @@ E: Fix langevin variable returned negative temperature Self-explanatory. +E: Fix langevin gjf with tbias is not yet implemented with kokkos + +This option is not yet available. + +W: Fix langevin gjf using random gaussians is not implemented with kokkos + +This will most likely cause errors in kinetic fluctuations. + */ diff --git a/src/fix_langevin.cpp b/src/fix_langevin.cpp index 1e86a90218..f805fddb4b 100644 --- a/src/fix_langevin.cpp +++ b/src/fix_langevin.cpp @@ -14,6 +14,9 @@ /* ---------------------------------------------------------------------- Contributing authors: Carolyn Phillips (U Mich), reservoir energy tally Aidan Thompson (SNL) GJF formulation + Charles Sievers & Niels Gronbech-Jensen (UC Davis) + updated GJF formulation and included + statistically correct 2GJ velocity ------------------------------------------------------------------------- */ #include "fix_langevin.h" @@ -35,6 +38,7 @@ #include "memory.h" #include "error.h" #include "group.h" +#include "utils.h" using namespace LAMMPS_NS; using namespace FixConst; @@ -50,7 +54,7 @@ enum{CONSTANT,EQUAL,ATOM}; FixLangevin::FixLangevin(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg), gjfflag(0), gfactor1(NULL), gfactor2(NULL), ratio(NULL), tstr(NULL), - flangevin(NULL), tforce(NULL), franprev(NULL), id_temp(NULL), random(NULL) + flangevin(NULL), tforce(NULL), franprev(NULL), lv(NULL), id_temp(NULL), random(NULL) { if (narg < 7) error->all(FLERR,"Illegal fix langevin command"); @@ -96,6 +100,7 @@ FixLangevin::FixLangevin(LAMMPS *lmp, int narg, char **arg) : oflag = 0; tallyflag = 0; zeroflag = 0; + osflag = 0; int iarg = 7; while (iarg < narg) { @@ -106,8 +111,15 @@ FixLangevin::FixLangevin(LAMMPS *lmp, int narg, char **arg) : iarg += 2; } else if (strcmp(arg[iarg],"gjf") == 0) { if (iarg+2 > narg) error->all(FLERR,"Illegal fix langevin command"); - if (strcmp(arg[iarg+1],"no") == 0) gjfflag = 0; - else if (strcmp(arg[iarg+1],"yes") == 0) gjfflag = 1; + if (strcmp(arg[iarg+1],"no") == 0) {gjfflag = 0; osflag = 0;} + else if (strcmp(arg[iarg+1],"vfull") == 0) { + gjfflag = 1; + osflag = 1; + } + else if (strcmp(arg[iarg+1],"vhalf") == 0) { + gjfflag = 1; + osflag = 0; + } else error->all(FLERR,"Illegal fix langevin command"); iarg += 2; } else if (strcmp(arg[iarg],"omega") == 0) { @@ -153,6 +165,7 @@ FixLangevin::FixLangevin(LAMMPS *lmp, int narg, char **arg) : flangevin = NULL; flangevin_allocated = 0; franprev = NULL; + lv = NULL; tforce = NULL; maxatom1 = maxatom2 = 0; @@ -161,7 +174,6 @@ FixLangevin::FixLangevin(LAMMPS *lmp, int narg, char **arg) : // no need to set peratom_flag, b/c data is for internal use only if (gjfflag) { - nvalues = 3; grow_arrays(atom->nmax); atom->add_callback(0); @@ -172,6 +184,9 @@ FixLangevin::FixLangevin(LAMMPS *lmp, int narg, char **arg) : franprev[i][0] = 0.0; franprev[i][1] = 0.0; franprev[i][2] = 0.0; + lv[i][0] = 0.0; + lv[i][1] = 0.0; + lv[i][2] = 0.0; } } @@ -192,6 +207,7 @@ FixLangevin::~FixLangevin() if (gjfflag) { memory->destroy(franprev); + memory->destroy(lv); atom->delete_callback(id,0); } } @@ -201,6 +217,7 @@ FixLangevin::~FixLangevin() int FixLangevin::setmask() { int mask = 0; + if (gjfflag) mask |= INITIAL_INTEGRATE; mask |= POST_FORCE; mask |= POST_FORCE_RESPA; mask |= END_OF_STEP; @@ -212,6 +229,21 @@ int FixLangevin::setmask() void FixLangevin::init() { + if (gjfflag){ + if (t_period*2 == update->dt) + error->all(FLERR,"Fix langevin gjf cannot have t_period equal to dt/2"); + + // warn if any integrate fix comes after this one + int before = 1; + int flag = 0; + for (int i = 0; i < modify->nfix; i++) { + if (strcmp(id,modify->fix[i]->id) == 0) before = 0; + else if ((modify->fmask[i] && utils::strmatch(modify->fix[i]->style,"^nve")) && before) flag = 1; + } + if (flag && comm->me == 0) + error->all(FLERR,"Fix langevin gjf should come before fix nve"); + } + if (oflag && !atom->sphere_flag) error->all(FLERR,"Fix langevin omega requires atom style sphere"); if (ascale && !atom->ellipsoid_flag) @@ -261,9 +293,14 @@ void FixLangevin::init() 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) / - force->ftm2v; + if (gjfflag) + gfactor2[i] = sqrt(atom->mass[i]) * + sqrt(2.0*force->boltz/t_period/update->dt/force->mvv2e) / + force->ftm2v; + else + gfactor2[i] = sqrt(atom->mass[i]) * + sqrt(24.0*force->boltz/t_period/update->dt/force->mvv2e) / + force->ftm2v; gfactor1[i] *= 1.0/ratio[i]; gfactor2[i] *= 1.0/sqrt(ratio[i]); } @@ -275,14 +312,60 @@ 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 (utils::strmatch(update->integrate_style,"^respa") && gjfflag) + error->all(FLERR,"Fix langevin gjf and respa are not compatible"); + if (gjfflag) gjfa = (1.0-update->dt/2.0/t_period)/(1.0+update->dt/2.0/t_period); + if (gjfflag) gjfsib = sqrt(1.0+update->dt/2.0/t_period); } /* ---------------------------------------------------------------------- */ void FixLangevin::setup(int vflag) { + if (gjfflag){ + double dtfm; + double dt = update->dt; + double **v = atom->v; + double **f = atom->f; + int *mask = atom->mask; + int nlocal = atom->nlocal; + double *rmass = atom->rmass; + double *mass = atom->mass; + int *type = atom->type; + if (rmass) { + for (int i = 0; i < nlocal; i++) + if (mask[i] & groupbit) { + dtfm = 0.5 * dt / rmass[i]; + v[i][0] -= dtfm * f[i][0]; + v[i][1] -= dtfm * f[i][1]; + v[i][2] -= dtfm * f[i][2]; + if (tbiasflag) + temperature->remove_bias(i,v[i]); + v[i][0] /= gjfa*gjfsib*gjfsib; + v[i][1] /= gjfa*gjfsib*gjfsib; + v[i][2] /= gjfa*gjfsib*gjfsib; + if (tbiasflag) + temperature->restore_bias(i,v[i]); + } + + } else { + for (int i = 0; i < nlocal; i++) + if (mask[i] & groupbit) { + dtfm = 0.5 * dt / mass[type[i]]; + v[i][0] -= dtfm * f[i][0]; + v[i][1] -= dtfm * f[i][1]; + v[i][2] -= dtfm * f[i][2]; + if (tbiasflag) + temperature->remove_bias(i,v[i]); + v[i][0] /= gjfa*gjfsib*gjfsib; + v[i][1] /= gjfa*gjfsib*gjfsib; + v[i][2] /= gjfa*gjfsib*gjfsib; + if (tbiasflag) + temperature->restore_bias(i,v[i]); + } + } + } if (strstr(update->integrate_style,"verlet")) post_force(vflag); else { @@ -290,6 +373,61 @@ void FixLangevin::setup(int vflag) post_force_respa(vflag,nlevels_respa-1,0); ((Respa *) update->integrate)->copy_f_flevel(nlevels_respa-1); } + if (gjfflag){ + double dtfm; + double dt = update->dt; + double **f = atom->f; + double **v = atom->v; + int *mask = atom->mask; + int nlocal = atom->nlocal; + double *rmass = atom->rmass; + double *mass = atom->mass; + int *type = atom->type; + if (rmass) { + for (int i = 0; i < nlocal; i++) + if (mask[i] & groupbit) { + dtfm = 0.5 * dt / rmass[i]; + v[i][0] += dtfm * f[i][0]; + v[i][1] += dtfm * f[i][1]; + v[i][2] += dtfm * f[i][2]; + lv[i][0] = v[i][0]; + lv[i][1] = v[i][1]; + lv[i][2] = v[i][2]; + } +// + } else { + for (int i = 0; i < nlocal; i++) + if (mask[i] & groupbit) { + dtfm = 0.5 * dt / mass[type[i]]; + v[i][0] += dtfm * f[i][0]; + v[i][1] += dtfm * f[i][1]; + v[i][2] += dtfm * f[i][2]; + lv[i][0] = v[i][0]; + lv[i][1] = v[i][1]; + lv[i][2] = v[i][2]; + } + } + } +} + +/* ---------------------------------------------------------------------- */ + +void FixLangevin::initial_integrate(int /* vflag */) +{ + double **v = atom->v; + double **f = atom->f; + int *mask = atom->mask; + int nlocal = atom->nlocal; + + for (int i = 0; i < nlocal; i++) + if (mask[i] & groupbit){ + f[i][0] /= gjfa; + f[i][1] /= gjfa; + f[i][2] /= gjfa; + v[i][0] = lv[i][0]; + v[i][1] = lv[i][1]; + v[i][2] = lv[i][2]; + } } /* ---------------------------------------------------------------------- */ @@ -304,7 +442,7 @@ void FixLangevin::post_force(int /*vflag*/) if (tstyle == ATOM) if (gjfflag) - if (tallyflag) + if (tallyflag || osflag) if (tbiasflag == BIAS) if (rmass) if (zeroflag) post_force_templated<1,1,1,1,1,1>(); @@ -511,7 +649,10 @@ 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; + if (Tp_GJF) + gamma2 = sqrt(rmass[i]) * sqrt(2.0*boltz/t_period/dt/mvv2e) / ftm2v; + else + gamma2 = sqrt(rmass[i]) * sqrt(24.0*boltz/t_period/dt/mvv2e) / ftm2v; gamma1 *= 1.0/ratio[type[i]]; gamma2 *= 1.0/sqrt(ratio[type[i]]) * tsqrt; } else { @@ -519,9 +660,16 @@ 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); + if (Tp_GJF){ + fran[0] = gamma2*random->gaussian(); + fran[1] = gamma2*random->gaussian(); + fran[2] = gamma2*random->gaussian(); + } + else{ + fran[0] = gamma2*(random->uniform()-0.5); + fran[1] = gamma2*(random->uniform()-0.5); + fran[2] = gamma2*(random->uniform()-0.5); + } if (Tp_BIAS) { temperature->remove_bias(i,v[i]); @@ -539,6 +687,16 @@ void FixLangevin::post_force_templated() } if (Tp_GJF) { + if (Tp_BIAS) + temperature->remove_bias(i,v[i]); + lv[i][0] = gjfsib*v[i][0]; + lv[i][1] = gjfsib*v[i][1]; + lv[i][2] = gjfsib*v[i][2]; + if (Tp_BIAS) + temperature->restore_bias(i,v[i]); + if (Tp_BIAS) + temperature->restore_bias(i,lv[i]); + fswap = 0.5*(fran[0]+franprev[i][0]); franprev[i][0] = fran[0]; fran[0] = fswap; @@ -549,32 +707,44 @@ void FixLangevin::post_force_templated() franprev[i][2] = fran[2]; fran[2] = fswap; - 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; + fdrag[0] *= gjfa; + fdrag[1] *= gjfa; + fdrag[2] *= gjfa; + fran[0] *= gjfa; + fran[1] *= gjfa; + fran[2] *= gjfa; + f[i][0] *= gjfa; + f[i][1] *= gjfa; + f[i][2] *= gjfa; } f[i][0] += fdrag[0] + fran[0]; f[i][1] += fdrag[1] + fran[1]; f[i][2] += fdrag[2] + fran[2]; - if (Tp_TALLY) { - flangevin[i][0] = fdrag[0] + fran[0]; - flangevin[i][1] = fdrag[1] + fran[1]; - flangevin[i][2] = fdrag[2] + fran[2]; - } - if (Tp_ZERO) { fsum[0] += fran[0]; fsum[1] += fran[1]; fsum[2] += fran[2]; } + + if (Tp_TALLY) { + if (Tp_GJF){ + fdrag[0] = gamma1*lv[i][0]/gjfsib/gjfsib; + fdrag[1] = gamma1*lv[i][1]/gjfsib/gjfsib; + fdrag[2] = gamma1*lv[i][2]/gjfsib/gjfsib; + fswap = (2*fran[0]/gjfa - franprev[i][0])/gjfsib; + fran[0] = fswap; + fswap = (2*fran[1]/gjfa - franprev[i][1])/gjfsib; + fran[1] = fswap; + fswap = (2*fran[2]/gjfa - franprev[i][2])/gjfsib; + fran[2] = fswap; + } + flangevin[i][0] = fdrag[0] + fran[0]; + flangevin[i][1] = fdrag[1] + fran[1]; + flangevin[i][2] = fdrag[2] + fran[2]; + + } } } @@ -754,18 +924,72 @@ void FixLangevin::angmom_thermostat() void FixLangevin::end_of_step() { - if (!tallyflag) return; + if (!tallyflag && !gjfflag) return; double **v = atom->v; int *mask = atom->mask; int nlocal = atom->nlocal; + double dtfm; + double dt = update->dt; + double *mass = atom->mass; + double *rmass = atom->rmass; + double **f = atom->f; + int *type = atom->type; 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]; + if (tallyflag){ + if (gjfflag){ + for (int i = 0; i < nlocal; i++) + if (mask[i] & groupbit) { + if (tbiasflag) + temperature->remove_bias(i, lv[i]); + energy_onestep += flangevin[i][0]*lv[i][0] + flangevin[i][1]*lv[i][1] + + flangevin[i][2]*lv[i][2]; + if (tbiasflag) + temperature->restore_bias(i, lv[i]); + } + } + else + 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]; + } + + if (gjfflag){ + double tmp[3]; + for (int i = 0; i < nlocal; i++) + if (mask[i] & groupbit){ + tmp[0] = v[i][0]; + tmp[1] = v[i][1]; + tmp[2] = v[i][2]; + if (!osflag){ + v[i][0] = lv[i][0]; + v[i][1] = lv[i][1]; + v[i][2] = lv[i][2]; + } + else{ + if (atom->rmass) { + dtfm = force->ftm2v * 0.5 * dt / rmass[i]; + } else { + dtfm = force->ftm2v * 0.5 * dt / mass[type[i]]; + } + v[i][0] = 0.5 * gjfsib*gjfsib*(v[i][0] + dtfm * f[i][0] / gjfa) + + dtfm * 0.5 * (gjfsib * flangevin[i][0] - franprev[i][0]) + + (gjfsib * gjfa * 0.5 + dt * 0.25 / t_period / gjfsib) * lv[i][0]; + v[i][1] = 0.5 * gjfsib*gjfsib*(v[i][1] + dtfm * f[i][1] / gjfa) + + dtfm * 0.5 * (gjfsib * flangevin[i][1] - franprev[i][1]) + + (gjfsib * gjfa * 0.5 + dt * 0.25 / t_period / gjfsib) * lv[i][1]; + v[i][2] = 0.5 * gjfsib*gjfsib*(v[i][2] + dtfm * f[i][2] / gjfa) + + dtfm * 0.5 * (gjfsib * flangevin[i][2] - franprev[i][2]) + + (gjfsib * gjfa * 0.5 + dt * 0.25 / t_period / gjfsib) * lv[i][2]; + } + lv[i][0] = tmp[0]; + lv[i][1] = tmp[1]; + lv[i][2] = tmp[2]; + } + } energy += energy_onestep*update->dt; } @@ -831,11 +1055,25 @@ double FixLangevin::compute_scalar() if (update->ntimestep == update->beginstep) { 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 = 0.5*energy_onestep*update->dt; + if (!gjfflag){ + 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 = 0.5*energy_onestep*update->dt; + } + else{ + for (int i = 0; i < nlocal; i++) + if (mask[i] & groupbit){ + if (tbiasflag) + temperature->remove_bias(i, lv[i]); + energy_onestep += flangevin[i][0]*lv[i][0] + flangevin[i][1]*lv[i][1] + + flangevin[i][2]*lv[i][2]; + if (tbiasflag) + temperature->restore_bias(i, lv[i]); + } + energy = -0.5*energy_onestep*update->dt; + } } // convert midstep energy back to previous fullstep energy @@ -867,8 +1105,8 @@ 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 (tallyflag) bytes += atom->nmax*3 * sizeof(double); + if (gjfflag) bytes += atom->nmax*6 * sizeof(double); + if (tallyflag || osflag) bytes += atom->nmax*3 * sizeof(double); if (tforce) bytes += atom->nmax * sizeof(double); return bytes; } @@ -880,6 +1118,7 @@ double FixLangevin::memory_usage() void FixLangevin::grow_arrays(int nmax) { memory->grow(franprev,nmax,3,"fix_langevin:franprev"); + memory->grow(lv,nmax,3,"fix_langevin:lv"); } /* ---------------------------------------------------------------------- @@ -888,8 +1127,12 @@ 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]; + lv[j][0] = lv[i][0]; + lv[j][1] = lv[i][1]; + lv[j][2] = lv[i][2]; } /* ---------------------------------------------------------------------- @@ -898,8 +1141,14 @@ 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++] = lv[i][0]; + buf[n++] = lv[i][1]; + buf[n++] = lv[i][2]; + return n; } /* ---------------------------------------------------------------------- @@ -908,6 +1157,12 @@ 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++]; + 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..868b71a44d 100644 --- a/src/fix_langevin.h +++ b/src/fix_langevin.h @@ -31,6 +31,7 @@ class FixLangevin : public Fix { int setmask(); void init(); void setup(int); + virtual void initial_integrate(int); virtual void post_force(int); void post_force_respa(int, int, int); virtual void end_of_step(); @@ -46,7 +47,7 @@ class FixLangevin : public Fix { int unpack_exchange(int, double *); protected: - int gjfflag,oflag,tallyflag,zeroflag,tbiasflag; + int gjfflag,nvalues,osflag,oflag,tallyflag,zeroflag,tbiasflag; int flangevin_allocated; double ascale; double t_start,t_stop,t_period,t_target; @@ -54,7 +55,7 @@ class FixLangevin : public Fix { double energy,energy_onestep; double tsqrt; int tstyle,tvar; - double gjffac; + double gjfa, gjfsib; //gjf a and gjf sqrt inverse b char *tstr; class AtomVecEllipsoid *avec; @@ -63,7 +64,7 @@ class FixLangevin : public Fix { double **flangevin; double *tforce; double **franprev; - int nvalues; + double **lv; //half step velocity char *id_temp; class Compute *temperature; @@ -139,6 +140,18 @@ E: Fix_modify temperature ID does not compute temperature The compute ID assigned to the fix must compute temperature. +E: Fix langevin gjf cannot have period equal to dt/2 + +If the period is equal to dt/2 then division by zero will happen. + +E: Fix langevin gjf should come before fix nve + +Self-explanatory + +E: Fix langevin gjf and respa are not compatible + +Self-explanatory + W: Group for fix_modify temp != fix group The fix_modify command is specifying a temperature computation that