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fix recenter/kk works with coords, init, null plus 3 tests

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This commit is contained in:
alphataubio
2024-07-30 04:28:40 -04:00
parent 53ae731e09
commit 4a972c4311
6 changed files with 171 additions and 37 deletions
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34
src/KOKKOS/fix_recenter_kokkos.cpp
View File

@ -37,9 +37,6 @@ template<class DeviceType>
FixRecenterKokkos<DeviceType>::FixRecenterKokkos(LAMMPS *lmp, int narg, char **arg) :
FixRecenter(lmp, narg, arg)
{
utils::logmesg(lmp, "************ FixRecenterKokkos constructor ************\n");
kokkosable = 1;
atomKK = (AtomKokkos *)atom;
execution_space = ExecutionSpaceFromDevice<DeviceType>::space;
@ -57,25 +54,15 @@ void FixRecenterKokkos<DeviceType>::initial_integrate(int /*vflag*/)
atomKK->sync(execution_space,datamask_read);
atomKK->modified(execution_space,datamask_modify);
x = atomKK->k_x.view<DeviceType>();
mask = atomKK->k_mask.view<DeviceType>();
d_x = atomKK->k_x.view<DeviceType>();
d_mask = atomKK->k_mask.view<DeviceType>();
int nlocal = atomKK->nlocal;
if (igroup == atomKK->firstgroup) nlocal = atomKK->nfirst;
// FIX RECENTER
// target COM
// bounding box around domain works for both orthogonal and triclinic
double xtarget = xinit;
double ytarget = yinit;
double ztarget = zinit;
xflag=yflag=zflag=1;
// FIXME: only supported in KOKKOS...
// fix ID group-ID recenter INIT INIT INIT shift all
/*
double xtarget,ytarget,ztarget;
double *bboxlo,*bboxhi;
if (scaleflag == FRACTION) {
@ -103,8 +90,6 @@ void FixRecenterKokkos<DeviceType>::initial_integrate(int /*vflag*/)
ztarget = bboxlo[2] + zcom*(bboxhi[2] - bboxlo[2]);
else ztarget = zcom;
*/
// current COM
// FIXME: make Group kokkos-aware
@ -127,18 +112,14 @@ void FixRecenterKokkos<DeviceType>::initial_integrate(int /*vflag*/)
shift[2] = zflag ? (ztarget - xcm[2]) : 0.0;
distance = sqrt(shift[0]*shift[0] + shift[1]*shift[1] + shift[2]*shift[2]);
// ----
copymode = 1;
//auto group2bit_copy = group2bit;
Kokkos::parallel_for(Kokkos::RangePolicy<DeviceType>(0,nlocal),
LAMMPS_LAMBDA(int i) {
if (mask[i] & group2bit) {
x(i,0) += shift[0];
x(i,1) += shift[1];
x(i,2) += shift[2];
if (d_mask[i] & group2bit) {
d_x(i,0) += shift[0];
d_x(i,1) += shift[1];
d_x(i,2) += shift[2];
}
});
@ -146,7 +127,6 @@ void FixRecenterKokkos<DeviceType>::initial_integrate(int /*vflag*/)
}
namespace LAMMPS_NS {
template class FixRecenterKokkos<LMPDeviceType>;
#ifdef LMP_KOKKOS_GPU

6
src/KOKKOS/fix_recenter_kokkos.h
View File

@ -28,8 +28,6 @@ FixStyle(recenter/kk/host,FixRecenterKokkos<LMPHostType>);
namespace LAMMPS_NS {
//struct TagFixRecenter {};
template<class DeviceType>
class FixRecenterKokkos : public FixRecenter {
public:
@ -38,8 +36,8 @@ class FixRecenterKokkos : public FixRecenter {
void initial_integrate(int) override;
private:
typename ArrayTypes<DeviceType>::t_x_array x;
typename ArrayTypes<DeviceType>::t_int_1d mask;
typename ArrayTypes<DeviceType>::t_x_array d_x;
typename ArrayTypes<DeviceType>::t_int_1d d_mask;
};
} // namespace LAMMPS_NS

4
src/fix_recenter.cpp
View File

@ -191,8 +191,6 @@ void FixRecenter::initial_integrate(int /*vflag*/)
group->xcm(igroup,masstotal,xcm);
utils::logmesg(lmp, "ok 2c, xcm={},{},{}\n", xcm[0], xcm[1], xcm[2]);
// shift coords by difference between actual COM and requested COM
double **x = atom->x;
@ -204,8 +202,6 @@ void FixRecenter::initial_integrate(int /*vflag*/)
shift[2] = zflag ? (ztarget - xcm[2]) : 0.0;
distance = sqrt(shift[0]*shift[0] + shift[1]*shift[1] + shift[2]*shift[2]);
utils::logmesg(lmp, "ok 2d, shift={},{},{}\n", shift[0], shift[1], shift[2]);
for (int i = 0; i < nlocal; i++)
if (mask[i] & group2bit) {
x[i][0] += shift[0];

80
unittest/force-styles/tests/fix-timestep-recenter-coords.yaml Normal file
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@ -0,0 +1,80 @@
---
lammps_version: 27 Jun 2024
tags: generated
date_generated: Tue Jul 30 04:23:44 2024
epsilon: 2e-13
skip_tests:
prerequisites: ! |
atom full
fix nve
fix recenter
pre_commands: ! ""
post_commands: ! |
fix move all nve
fix test solute recenter 0.45 0.5 0.55 shift all units fraction
input_file: in.fourmol
natoms: 29
global_scalar: 4.868395120178045e-05
global_vector: ! |-
3 -4.5648814136156624e-05 -3.3198799039568794e-06 1.6591903748613968e-05
run_pos: ! |2
1 -7.5132769500671226e-01 2.4986248943444171e+00 7.9802680459215103e-01
2 -1.7083180151387659e-01 2.9686443668858833e+00 1.1032169213735510e-01
3 -1.1848576112607669e+00 1.2379598993595067e+00 3.3721005306300700e-01
4 -2.0626880309028004e+00 1.4911496856694382e+00 -2.8888576109863040e-01
5 -1.3880697339807648e+00 9.3392994263319751e-01 1.3645274273913177e+00
6 -2.3255489200431190e-01 2.9053911875515726e-01 -2.6643801066357575e-01
7 -1.3943682083900774e-01 -1.5237647264946797e-02 -1.5642438189827357e+00
8 6.9348312565712877e-01 -4.8122338188209490e-01 3.2715099339931453e-01
9 8.9918032569715922e-01 -2.4533830652762220e-01 1.2485251813785214e+00
10 1.5702044248015166e+00 -1.4529974702538417e+00 -1.8252128309559742e-02
11 1.3069310971913839e+00 -1.9847774235184412e+00 -9.2407492225500776e-01
12 2.5254286066811331e+00 -4.8272460119318827e-01 -6.5820448823105326e-01
13 3.5706681986664290e+00 -8.8461121229009532e-01 -6.7501523048492595e-01
14 2.1258242373015102e+00 -4.1048363587869696e-01 -1.6984150383718699e+00
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16 2.1938308722699804e+00 -2.4050030016799853e+00 9.4154957635695380e-01
17 1.7344856812755074e+00 -2.0823896149143275e+00 2.1613004019555140e+00
18 1.6560980731586978e+00 3.0232596451395048e+00 -2.5529495112139315e+00
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25 8.2366303589634160e-01 3.2739214743607290e+00 3.4761708482509213e+00
26 2.1000516430182552e+00 4.0191691643247269e+00 4.1861913754165592e+00
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29 -1.7934721163888576e+00 -3.5888429001718487e+00 3.2396195693813534e+00
run_vel: ! |2
1 8.1705744183262520e-03 1.6516406176274312e-02 4.7902264318912926e-03
2 5.4501493445687594e-03 5.1791699408496325e-03 -1.4372931530376343e-03
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27 4.5604120293371412e-04 -1.0305523026921115e-03 2.1188058381359324e-04
28 -6.2544520861855810e-03 1.4127711176147026e-03 -1.8429821884794668e-03
29 6.4110631534402326e-04 3.1273432719593694e-03 3.7253671105656788e-03
...

4
unittest/force-styles/tests/fix-timestep-recenter.yaml → unittest/force-styles/tests/fix-timestep-recenter-init.yaml
View File

@ -1,7 +1,7 @@
---
lammps_version: 27 Jun 2024
tags: generated
date_generated: Tue Jul 30 03:14:33 2024
date_generated: Tue Jul 30 04:14:01 2024
epsilon: 2e-13
skip_tests:
prerequisites: ! |
@ -11,7 +11,7 @@ prerequisites: ! |
pre_commands: ! ""
post_commands: ! |
fix move all nve
fix test solute recenter INIT INIT INIT shift all
fix test solute recenter INIT INIT INIT shift all units box
input_file: in.fourmol
natoms: 29
global_scalar: 4.868395120232176e-05

80
unittest/force-styles/tests/fix-timestep-recenter-null.yaml Normal file
View File

@ -0,0 +1,80 @@
---
lammps_version: 27 Jun 2024
tags: generated
date_generated: Tue Jul 30 04:25:52 2024
epsilon: 2e-13
skip_tests:
prerequisites: ! |
atom full
fix nve
fix recenter
pre_commands: ! ""
post_commands: ! |
fix move all nve
fix test solute recenter NULL NULL NULL shift all units lattice
input_file: in.fourmol
natoms: 29
global_scalar: 0
global_vector: ! |-
3 0 0 0
run_pos: ! |2
1 -2.7045559775384032e-01 2.4912159905679729e+00 -1.6695851791541888e-01
2 3.1004029573899528e-01 2.9612354631094391e+00 -8.5466363037021464e-01
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run_vel: ! |2
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...