Merge pull request lammps#4346 from cjknight/lubricate_patch

features + bug fixes for granular simulations w/ Kokkos

doc/src/Commands_pair.rst

@@ -44,7 +44,7 @@ OPT.
    * :doc:`born/coul/wolf/cs (g) <pair_cs>`
    * :doc:`born/gauss <pair_born_gauss>`
    * :doc:`bpm/spring <pair_bpm_spring>`
-   * :doc:`brownian (o) <pair_brownian>`
+   * :doc:`brownian (ko) <pair_brownian>`
    * :doc:`brownian/poly (o) <pair_brownian>`
    * :doc:`buck (giko) <pair_buck>`
    * :doc:`buck/coul/cut (giko) <pair_buck>`

doc/src/pair_brownian.rst

@@ -1,12 +1,13 @@
 .. index:: pair_style brownian
 .. index:: pair_style brownian/omp
+.. index:: pair_style brownian/kk
 .. index:: pair_style brownian/poly
 .. index:: pair_style brownian/poly/omp
 
 pair_style brownian command
 ===========================
 
-Accelerator Variants: *brownian/omp*
+Accelerator Variants: *brownian/omp*, *brownian/kk*
 
 pair_style brownian/poly command
 ================================

src/COLLOID/pair_brownian.cpp

@@ -54,6 +54,8 @@ PairBrownian::PairBrownian(LAMMPS *lmp) : Pair(lmp)
 
 PairBrownian::~PairBrownian()
 {
+  if (copymode) return;
+
   if (allocated) {
     memory->destroy(setflag);
     memory->destroy(cutsq);

src/COLLOID/pair_brownian.h

@@ -31,7 +31,7 @@ class PairBrownian : public Pair {
   void compute(int, int) override;
   void settings(int, char **) override;
   void coeff(int, char **) override;
-  double init_one(int, int) override;
+  virtual double init_one(int, int) override;
   void init_style() override;
   void write_restart(FILE *) override;
   void read_restart(FILE *) override;
@@ -55,7 +55,7 @@ class PairBrownian : public Pair {
   class RanMars *random;
 
   void set_3_orthogonal_vectors(double *, double *, double *);
-  void allocate();
+  virtual void allocate();
 };
 
 }    // namespace LAMMPS_NS

src/KOKKOS/Install.sh

@@ -277,6 +277,8 @@ action npair_trim_kokkos.h
 action pack_kokkos.h pack.h
 action pair_adp_kokkos.cpp pair_adp.cpp
 action pair_adp_kokkos.h pair_adp.h
+action pair_brownian_kokkos.cpp pair_brownian.cpp
+action pair_brownian_kokkos.h pair_brownian.h
 action pair_buck_coul_cut_kokkos.cpp
 action pair_buck_coul_cut_kokkos.h
 action pair_buck_coul_long_kokkos.cpp pair_buck_coul_long.cpp

src/KOKKOS/compute_temp_deform_kokkos.cpp

@@ -190,10 +190,20 @@ void ComputeTempDeformKokkos<DeviceType>::operator()(TagComputeTempDeformVector<
 }
 
 /* ---------------------------------------------------------------------- */
+
 template<class DeviceType>
 void ComputeTempDeformKokkos<DeviceType>::remove_bias_all()
 {
-  atomKK->sync(execution_space,datamask_read);
+  remove_bias_all_kk();
+  atomKK->sync(Host,V_MASK);
+}
+
+/* ---------------------------------------------------------------------- */
+
+template<class DeviceType>
+void ComputeTempDeformKokkos<DeviceType>::remove_bias_all_kk()
+{
+  atomKK->sync(execution_space,X_MASK|V_MASK);
   v = atomKK->k_v.view<DeviceType>();
   x = atomKK->k_x.view<DeviceType>();
   mask = atomKK->k_mask.view<DeviceType>();
@@ -214,6 +224,8 @@ void ComputeTempDeformKokkos<DeviceType>::remove_bias_all()
   copymode = 0;
 
   domainKK->lamda2x(nlocal);
+
+  atomKK->modified(execution_space,V_MASK);
 }
 
 template<class DeviceType>
@@ -230,18 +242,20 @@ void ComputeTempDeformKokkos<DeviceType>::operator()(TagComputeTempDeformRemoveB
 }
 
 /* ---------------------------------------------------------------------- */
+
 template<class DeviceType>
 void ComputeTempDeformKokkos<DeviceType>::restore_bias_all()
 {
-  atomKK->sync(execution_space,datamask_read);
+  atomKK->sync(execution_space,V_MASK);
   v = atomKK->k_v.view<DeviceType>();
-  x = atomKK->k_x.view<DeviceType>();
   mask = atomKK->k_mask.view<DeviceType>();
   int nlocal = atom->nlocal;
 
   copymode = 1;
   Kokkos::parallel_for(Kokkos::RangePolicy<DeviceType, TagComputeTempDeformRestoreBias >(0,nlocal),*this);
   copymode = 0;
+
+  atomKK->modified(execution_space,V_MASK);
 }
 
 template<class DeviceType>

src/KOKKOS/compute_temp_deform_kokkos.h

@@ -69,6 +69,7 @@ class ComputeTempDeformKokkos: public ComputeTempDeform {
   double compute_scalar() override;
   void compute_vector() override;
   void remove_bias_all() override;
+  void remove_bias_all_kk() override;
   void restore_bias_all() override;
 
   template<int RMASS>

src/KOKKOS/fix_deform_kokkos.cpp

@@ -55,7 +55,11 @@ void FixDeformKokkos::pre_exchange()
 
 void FixDeformKokkos::end_of_step()
 {
-  atomKK->sync(Host,ALL_MASK);
+  if (remapflag == Domain::X_REMAP && rfix.size() > 0)
+    atomKK->sync(Host,ALL_MASK);
+
   FixDeform::end_of_step();
-  atomKK->modified(Host,ALL_MASK);
+
+  if (remapflag == Domain::X_REMAP && rfix.size() > 0)
+    atomKK->modified(Host,ALL_MASK);
 }

src/KOKKOS/fix_langevin_kokkos.cpp

@@ -86,7 +86,6 @@ FixLangevinKokkos<DeviceType>::FixLangevinKokkos(LAMMPS *lmp, int narg, char **a
   execution_space = ExecutionSpaceFromDevice<DeviceType>::space;
   datamask_read =  V_MASK | F_MASK | MASK_MASK | RMASS_MASK | TYPE_MASK;
   datamask_modify = F_MASK;
-
 }
 
 /* ---------------------------------------------------------------------- */
@@ -227,12 +226,16 @@ void FixLangevinKokkos<DeviceType>::post_force(int /*vflag*/)
 
   // account for bias velocity
   if (tbiasflag == BIAS) {
-    atomKK->sync(temperature->execution_space,temperature->datamask_read);
-    temperature->compute_scalar();
-    temperature->remove_bias_all(); // modifies velocities
-    // 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);
+    if (temperature->kokkosable) {
+      temperature->compute_scalar();
+      temperature->remove_bias_all_kk();
+    } else {
+      atomKK->sync(temperature->execution_space,temperature->datamask_read);
+      temperature->compute_scalar();
+      temperature->remove_bias_all();
+      atomKK->modified(temperature->execution_space,temperature->datamask_modify);
+      atomKK->sync(execution_space,temperature->datamask_modify);
+    }
   }
 
   // compute langevin force in parallel on the device
@@ -526,10 +529,13 @@ void FixLangevinKokkos<DeviceType>::post_force(int /*vflag*/)
 
 
   if (tbiasflag == BIAS) {
-    atomKK->sync(temperature->execution_space,temperature->datamask_read);
-    temperature->restore_bias_all(); // modifies velocities
-    atomKK->modified(temperature->execution_space,temperature->datamask_modify);
-    atomKK->sync(execution_space,temperature->datamask_modify);
+    if (temperature->kokkosable) temperature->restore_bias_all();
+    else {
+      atomKK->sync(temperature->execution_space,temperature->datamask_read);
+      temperature->restore_bias_all();
+      atomKK->modified(temperature->execution_space,temperature->datamask_modify);
+      atomKK->sync(execution_space,temperature->datamask_modify);
+    }
   }
 
   // set modify flags for the views modified in post_force functor

src/KOKKOS/fix_nh_kokkos.cpp

@@ -80,7 +80,11 @@ void FixNHKokkos<DeviceType>::setup(int /*vflag*/)
 {
   // tdof needed by compute_temp_target()
 
+  atomKK->sync(temperature->execution_space,temperature->datamask_read);
   t_current = temperature->compute_scalar();
+  atomKK->modified(temperature->execution_space,temperature->datamask_modify);
+  atomKK->sync(execution_space,temperature->datamask_modify);
+
   tdof = temperature->dof;
 
   // t_target is needed by NPH and NPT in compute_scalar()
@@ -105,6 +109,7 @@ void FixNHKokkos<DeviceType>::setup(int /*vflag*/)
         atomKK->sync(temperature->execution_space,temperature->datamask_read);
         t0 = temperature->compute_scalar();
         atomKK->modified(temperature->execution_space,temperature->datamask_modify);
+        atomKK->sync(execution_space,temperature->datamask_modify);
         if (t0 < EPSILON)
           error->all(FLERR,"Current temperature too close to zero, consider using ptemp keyword");
       }
@@ -117,6 +122,8 @@ void FixNHKokkos<DeviceType>::setup(int /*vflag*/)
   atomKK->sync(temperature->execution_space,temperature->datamask_read);
   t_current = temperature->compute_scalar();
   atomKK->modified(temperature->execution_space,temperature->datamask_modify);
+  atomKK->sync(execution_space,temperature->datamask_modify);
+
   tdof = temperature->dof;
 
   if (pstat_flag) {
@@ -194,16 +201,18 @@ void FixNHKokkos<DeviceType>::initial_integrate(int /*vflag*/)
 
   if (pstat_flag) {
     atomKK->sync(temperature->execution_space,temperature->datamask_read);
-    atomKK->modified(temperature->execution_space,temperature->datamask_modify);
-    //atomKK->sync(pressure->execution_space,pressure->datamask_read);
-    //atomKK->modified(pressure->execution_space,pressure->datamask_modify);
+    atomKK->sync(pressure->execution_space,pressure->datamask_read);
     if (pstyle == ISO) {
       temperature->compute_scalar();
       pressure->compute_scalar();
     } else {
       temperature->compute_vector();
       pressure->compute_vector();
     }
+    atomKK->modified(temperature->execution_space,temperature->datamask_modify);
+    atomKK->modified(pressure->execution_space,pressure->datamask_modify);
+    atomKK->sync(execution_space,temperature->datamask_modify);
+    atomKK->sync(execution_space,pressure->datamask_modify);
     couple();
     pressure->addstep(update->ntimestep+1);
   }
@@ -250,6 +259,7 @@ void FixNHKokkos<DeviceType>::final_integrate()
     atomKK->sync(temperature->execution_space,temperature->datamask_read);
     t_current = temperature->compute_scalar();
     atomKK->modified(temperature->execution_space,temperature->datamask_modify);
+    atomKK->sync(execution_space,temperature->datamask_modify);
   }
 
   if (pstat_flag) nh_v_press();
@@ -260,15 +270,24 @@ void FixNHKokkos<DeviceType>::final_integrate()
   atomKK->sync(temperature->execution_space,temperature->datamask_read);
   t_current = temperature->compute_scalar();
   atomKK->modified(temperature->execution_space,temperature->datamask_modify);
+  atomKK->sync(execution_space,temperature->datamask_modify);
   tdof = temperature->dof;
 
   if (pstat_flag) {
-    //atomKK->sync(pressure->execution_space,pressure->datamask_read);
-    //atomKK->modified(pressure->execution_space,pressure->datamask_modify);
-    if (pstyle == ISO) pressure->compute_scalar();
-    else {
+    if (pstyle == ISO) {
+      atomKK->sync(pressure->execution_space,pressure->datamask_read);
+      pressure->compute_scalar();
+      atomKK->modified(pressure->execution_space,pressure->datamask_modify);
+      atomKK->sync(execution_space,pressure->datamask_modify);
+    } else {
+      atomKK->sync(temperature->execution_space,temperature->datamask_read);
+      atomKK->sync(pressure->execution_space,pressure->datamask_read);
       temperature->compute_vector();
       pressure->compute_vector();
+      atomKK->modified(temperature->execution_space,temperature->datamask_modify);
+      atomKK->modified(pressure->execution_space,pressure->datamask_modify);
+      atomKK->sync(execution_space,temperature->datamask_modify);
+      atomKK->sync(execution_space,pressure->datamask_modify);
     }
     couple();
     pressure->addstep(update->ntimestep+1);
@@ -480,9 +499,13 @@ void FixNHKokkos<DeviceType>::nh_v_press()
   factor[2] = exp(-dt4*(omega_dot[2]+mtk_term2));
 
   if (which == BIAS) {
-    atomKK->sync(temperature->execution_space,temperature->datamask_read);
-    temperature->remove_bias_all();
-    atomKK->modified(temperature->execution_space,temperature->datamask_modify);
+    if (temperature->kokkosable) temperature->remove_bias_all_kk();
+    else {
+      atomKK->sync(temperature->execution_space,temperature->datamask_read);
+      temperature->remove_bias_all();
+      atomKK->modified(temperature->execution_space,temperature->datamask_modify);
+      atomKK->sync(execution_space,temperature->datamask_modify);
+    }
   }
 
   atomKK->sync(execution_space,V_MASK | MASK_MASK);
@@ -497,11 +520,14 @@ void FixNHKokkos<DeviceType>::nh_v_press()
   atomKK->modified(execution_space,V_MASK);
 
   if (which == BIAS) {
-    atomKK->sync(temperature->execution_space,temperature->datamask_read);
-    temperature->restore_bias_all();
-    atomKK->modified(temperature->execution_space,temperature->datamask_modify);
+    if (temperature->kokkosable) temperature->restore_bias_all();
+    else {
+      atomKK->sync(temperature->execution_space,temperature->datamask_read);
+      temperature->restore_bias_all();
+      atomKK->modified(temperature->execution_space,temperature->datamask_modify);
+      atomKK->sync(execution_space,temperature->datamask_modify);
+    }
   }
-
 }
 
 template<class DeviceType>
@@ -617,9 +643,13 @@ void FixNHKokkos<DeviceType>::nh_v_temp()
   if (igroup == atomKK->firstgroup) nlocal = atomKK->nfirst;
 
   if (which == BIAS) {
-    atomKK->sync(temperature->execution_space,temperature->datamask_read);
-    temperature->remove_bias_all();
-    atomKK->modified(temperature->execution_space,temperature->datamask_modify);
+    if (temperature->kokkosable) temperature->remove_bias_all_kk();
+    else {
+      atomKK->sync(temperature->execution_space,temperature->datamask_read);
+      temperature->remove_bias_all();
+      atomKK->modified(temperature->execution_space,temperature->datamask_modify);
+      atomKK->sync(execution_space,temperature->datamask_modify);
+    }
   }
 
   atomKK->sync(execution_space,V_MASK | MASK_MASK);
@@ -631,9 +661,13 @@ void FixNHKokkos<DeviceType>::nh_v_temp()
   atomKK->modified(execution_space,V_MASK);
 
   if (which == BIAS) {
-    atomKK->sync(temperature->execution_space,temperature->datamask_read);
-    temperature->restore_bias_all();
-    atomKK->modified(temperature->execution_space,temperature->datamask_modify);
+    if (temperature->kokkosable) temperature->restore_bias_all();
+    else {
+      atomKK->sync(temperature->execution_space,temperature->datamask_read);
+      temperature->restore_bias_all();
+      atomKK->modified(temperature->execution_space,temperature->datamask_modify);
+      atomKK->sync(execution_space,temperature->datamask_modify);
+    }
   }
 }