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Merge pull request #4190 from alphataubio/kokkos-unit-testing

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Improve Kokkos unit testing
This commit is contained in:
Axel Kohlmeyer
2024-09-30 19:50:08 -04:00
committed by GitHub
parent ec2fece8db db4c6fbaaa
commit 75f86a68a7
47 changed files with 1748 additions and 930 deletions
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8
lib/kokkos/Makefile.kokkos
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@ -23,7 +23,7 @@ KOKKOS_DEVICES ?= "OpenMP"
# NVIDIA: Kepler,Kepler30,Kepler32,Kepler35,Kepler37,Maxwell,Maxwell50,Maxwell52,Maxwell53,Pascal60,Pascal61,Volta70,Volta72,Turing75,Ampere80,Ampere86,Ada89,Hopper90
# ARM: ARMv80,ARMv81,ARMv8-ThunderX,ARMv8-TX2,A64FX,ARMv9-Grace
# IBM: Power8,Power9
# AMD-GPUS: AMD_GFX906,AMD_GFX908,AMD_GFX90A,AMD_GFX940,AMD_GFX942,AMD_GFX1030,AMD_GFX1100
# AMD-GPUS: AMD_GFX906,AMD_GFX908,AMD_GFX90A,AMD_GFX940,AMD_GFX942,AMD_GFX1030,AMD_GFX1100,AMD_GFX1103
# AMD-CPUS: AMDAVX,Zen,Zen2,Zen3
# Intel-GPUs: Intel_Gen,Intel_Gen9,Intel_Gen11,Intel_Gen12LP,Intel_DG1,Intel_XeHP,Intel_PVC
KOKKOS_ARCH ?= ""
@ -465,6 +465,7 @@ KOKKOS_INTERNAL_USE_ARCH_AMD_GFX1100 := $(call kokkos_has_string,$(KOKKOS_ARCH),
ifeq ($(KOKKOS_INTERNAL_USE_ARCH_AMD_GFX1100), 0)
KOKKOS_INTERNAL_USE_ARCH_AMD_GFX1100 := $(call kokkos_has_string,$(KOKKOS_ARCH),NAVI1100)
endif
KOKKOS_INTERNAL_USE_ARCH_AMD_GFX1103 := $(call kokkos_has_string,$(KOKKOS_ARCH),AMD_GFX1103)
# Any AVX?
KOKKOS_INTERNAL_USE_ARCH_AVX := $(shell expr $(KOKKOS_INTERNAL_USE_ARCH_SNB) + $(KOKKOS_INTERNAL_USE_ARCH_AMDAVX))
@ -1158,6 +1159,11 @@ ifeq ($(KOKKOS_INTERNAL_USE_ARCH_AMD_GFX1100), 1)
tmp := $(call kokkos_append_header,"$H""define KOKKOS_ARCH_AMD_GPU")
KOKKOS_INTERNAL_HIP_ARCH_FLAG := --offload-arch=gfx1100
endif
ifeq ($(KOKKOS_INTERNAL_USE_ARCH_AMD_GFX1103), 1)
tmp := $(call kokkos_append_header,"$H""define KOKKOS_ARCH_AMD_GFX1103")
tmp := $(call kokkos_append_header,"$H""define KOKKOS_ARCH_AMD_GPU")
KOKKOS_INTERNAL_HIP_ARCH_FLAG := --offload-arch=gfx1103
endif
ifeq ($(KOKKOS_INTERNAL_USE_HIP), 1)

1
lib/kokkos/cmake/KokkosCore_config.h.in
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@ -120,6 +120,7 @@
#cmakedefine KOKKOS_ARCH_AMD_GFX942
#cmakedefine KOKKOS_ARCH_AMD_GFX1030
#cmakedefine KOKKOS_ARCH_AMD_GFX1100
#cmakedefine KOKKOS_ARCH_AMD_GFX1103
#cmakedefine KOKKOS_ARCH_AMD_GPU
#cmakedefine KOKKOS_ARCH_VEGA // deprecated
#cmakedefine KOKKOS_ARCH_VEGA906 // deprecated

6
lib/kokkos/cmake/kokkos_arch.cmake
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@ -103,9 +103,9 @@ LIST(APPEND CORRESPONDING_AMD_FLAGS gfx90a gfx90a gfx908 gfx908)
LIST(APPEND SUPPORTED_AMD_GPUS MI50/60 MI50/60)
LIST(APPEND SUPPORTED_AMD_ARCHS VEGA906 AMD_GFX906)
LIST(APPEND CORRESPONDING_AMD_FLAGS gfx906 gfx906)
LIST(APPEND SUPPORTED_AMD_GPUS RX7900XTX RX7900XTX V620/W6800 V620/W6800)
LIST(APPEND SUPPORTED_AMD_ARCHS NAVI1100 AMD_GFX1100 NAVI1030 AMD_GFX1030)
LIST(APPEND CORRESPONDING_AMD_FLAGS gfx1100 gfx1100 gfx1030 gfx1030)
LIST(APPEND SUPPORTED_AMD_GPUS PHOENIX RX7900XTX V620/W6800 V620/W6800)
LIST(APPEND SUPPORTED_AMD_ARCHS AMD_GFX1103 AMD_GFX1100 NAVI1030 AMD_GFX1030)
LIST(APPEND CORRESPONDING_AMD_FLAGS gfx1103 gfx1100 gfx1030 gfx1030)
#FIXME CAN BE REPLACED WITH LIST_ZIP IN CMAKE 3.17
FOREACH(ARCH IN LISTS SUPPORTED_AMD_ARCHS)

3
lib/kokkos/core/src/HIP/Kokkos_HIP_Instance.hpp
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@ -35,7 +35,8 @@ struct HIPTraits {
static constexpr int WarpSize = 64;
static constexpr int WarpIndexMask = 0x003f; /* hexadecimal for 63 */
static constexpr int WarpIndexShift = 6; /* WarpSize == 1 << WarpShift*/
#elif defined(KOKKOS_ARCH_AMD_GFX1030) || defined(KOKKOS_ARCH_AMD_GFX1100)
#elif defined(KOKKOS_ARCH_AMD_GFX1030) || defined(KOKKOS_ARCH_AMD_GFX1100) || \
defined(KOKKOS_ARCH_AMD_GFX1103)
static constexpr int WarpSize = 32;
static constexpr int WarpIndexMask = 0x001f; /* hexadecimal for 31 */
static constexpr int WarpIndexShift = 5; /* WarpSize == 1 << WarpShift*/

2
lib/kokkos/core/src/OpenMPTarget/Kokkos_OpenMPTarget_ParallelScan_Range.hpp
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@ -143,7 +143,7 @@ class ParallelScan<FunctorType, Kokkos::RangePolicy<Traits...>,
local_offset_value = element_values(team_id, i - 1);
// FIXME_OPENMPTARGET We seem to access memory illegaly on AMD GPUs
#if defined(KOKKOS_ARCH_AMD_GPU) && !defined(KOKKOS_ARCH_AMD_GFX1030) && \
!defined(KOKKOS_ARCH_AMD_GFX1100)
!defined(KOKKOS_ARCH_AMD_GFX1100) && !defined(KOKKOS_ARCH_AMD_GFX1103)
if constexpr (Analysis::Reducer::has_join_member_function()) {
if constexpr (std::is_void_v<WorkTag>)
a_functor_reducer.get_functor().join(local_offset_value,

3
lib/kokkos/core/src/impl/Kokkos_Core.cpp
View File

@ -752,6 +752,9 @@ void pre_initialize_internal(const Kokkos::InitializationSettings& settings) {
#elif defined(KOKKOS_ARCH_AMD_GFX1100)
declare_configuration_metadata("architecture", "GPU architecture",
"AMD_GFX1100");
#elif defined(KOKKOS_ARCH_AMD_GFX1103)
declare_configuration_metadata("architecture", "GPU architecture",
"AMD_GFX1103");
#else
declare_configuration_metadata("architecture", "GPU architecture", "none");

1
lib/kokkos/generate_makefile.bash
View File

@ -164,6 +164,7 @@ display_help_text() {
echo " AMD_GFX942 = AMD GPU MI300 GFX942"
echo " AMD_GFX1030 = AMD GPU V620/W6800 GFX1030"
echo " AMD_GFX1100 = AMD GPU RX 7900 XT(X) GFX1100"
echo " AMD_GFX1103 = AMD APU Radeon 740M/760M/780M/880M/890M GFX1103"
echo " [ARM]"
echo " ARMV80 = ARMv8.0 Compatible CPU"
echo " ARMV81 = ARMv8.1 Compatible CPU"

56
src/KOKKOS/domain_kokkos.cpp
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@ -563,7 +563,6 @@ void DomainKokkos::operator()(TagDomain_image_flip, const int &i) const {
void DomainKokkos::lamda2x(int n)
{
atomKK->sync(Device,X_MASK);
x = atomKK->k_x.view<LMPDeviceType>();
copymode = 1;
@ -573,6 +572,21 @@ void DomainKokkos::lamda2x(int n)
atomKK->modified(Device,X_MASK);
}
void DomainKokkos::lamda2x(int n, int groupbit_in)
{
atomKK->sync(Device,X_MASK);
x = atomKK->k_x.view<LMPDeviceType>();
mask = atomKK->k_mask.view<LMPDeviceType>();
mask = atomKK->k_mask.view<LMPDeviceType>();
groupbit = groupbit_in;
copymode = 1;
Kokkos::parallel_for(Kokkos::RangePolicy<LMPDeviceType, TagDomain_lamda2x_group>(0,n),*this);
copymode = 0;
atomKK->modified(Device,X_MASK);
}
KOKKOS_INLINE_FUNCTION
void DomainKokkos::operator()(TagDomain_lamda2x, const int &i) const {
const double xi1 = x(i,1);
@ -582,6 +596,17 @@ void DomainKokkos::operator()(TagDomain_lamda2x, const int &i) const {
x(i,2) = h[2]*xi2 + boxlo[2];
}
KOKKOS_INLINE_FUNCTION
void DomainKokkos::operator()(TagDomain_lamda2x_group, const int &i) const {
if (mask[i] & groupbit) {
const double xi1 = x(i,1);
const double xi2 = x(i,2);
x(i,0) = h[0]*x(i,0) + h[5]*xi1 + h[4]*xi2 + boxlo[0];
x(i,1) = h[1]*xi1 + h[3]*xi2 + boxlo[1];
x(i,2) = h[2]*xi2 + boxlo[2];
}
}
/* ----------------------------------------------------------------------
convert box coords to triclinic 0-1 lamda coords for all N atoms
lamda = H^-1 (x - x0)
@ -590,7 +615,6 @@ void DomainKokkos::operator()(TagDomain_lamda2x, const int &i) const {
void DomainKokkos::x2lamda(int n)
{
atomKK->sync(Device,X_MASK);
x = atomKK->k_x.view<LMPDeviceType>();
copymode = 1;
@ -600,6 +624,20 @@ void DomainKokkos::x2lamda(int n)
atomKK->modified(Device,X_MASK);
}
void DomainKokkos::x2lamda(int n, int groupbit_in)
{
atomKK->sync(Device,X_MASK);
x = atomKK->k_x.view<LMPDeviceType>();
mask = atomKK->k_mask.view<LMPDeviceType>();
groupbit = groupbit_in;
copymode = 1;
Kokkos::parallel_for(Kokkos::RangePolicy<LMPDeviceType, TagDomain_x2lamda_group>(0,n),*this);
copymode = 0;
atomKK->modified(Device,X_MASK);
}
KOKKOS_INLINE_FUNCTION
void DomainKokkos::operator()(TagDomain_x2lamda, const int &i) const {
F_FLOAT delta[3];
@ -612,3 +650,17 @@ void DomainKokkos::operator()(TagDomain_x2lamda, const int &i) const {
x(i,2) = h_inv[2]*delta[2];
}
KOKKOS_INLINE_FUNCTION
void DomainKokkos::operator()(TagDomain_x2lamda_group, const int &i) const {
if (mask[i] & groupbit) {
F_FLOAT delta[3];
delta[0] = x(i,0) - boxlo[0];
delta[1] = x(i,1) - boxlo[1];
delta[2] = x(i,2) - boxlo[2];
x(i,0) = h_inv[0]*delta[0] + h_inv[5]*delta[1] + h_inv[4]*delta[2];
x(i,1) = h_inv[1]*delta[1] + h_inv[3]*delta[2];
x(i,2) = h_inv[2]*delta[2];
}
}

12
src/KOKKOS/domain_kokkos.h
View File

@ -24,7 +24,9 @@ namespace LAMMPS_NS {
struct TagDomain_remap_all{};
struct TagDomain_image_flip{};
struct TagDomain_lamda2x{};
struct TagDomain_lamda2x_group{};
struct TagDomain_x2lamda{};
struct TagDomain_x2lamda_group{};
class DomainKokkos : public Domain {
public:
@ -35,7 +37,9 @@ class DomainKokkos : public Domain {
void remap_all();
void image_flip(int, int, int);
void x2lamda(int) override;
void x2lamda(int,int) override;
void lamda2x(int) override;
void lamda2x(int,int) override;
// forward remaining x2lamda() and lambda2x() variants to parent class
void x2lamda(double *a, double *b) override { Domain::x2lamda(a,b); }
void lamda2x(double *a, double *b) override { Domain::lamda2x(a,b); }
@ -54,18 +58,26 @@ class DomainKokkos : public Domain {
KOKKOS_INLINE_FUNCTION
void operator()(TagDomain_lamda2x, const int&) const;
KOKKOS_INLINE_FUNCTION
void operator()(TagDomain_lamda2x_group, const int&) const;
KOKKOS_INLINE_FUNCTION
void operator()(TagDomain_x2lamda, const int&) const;
KOKKOS_INLINE_FUNCTION
void operator()(TagDomain_x2lamda_group, const int&) const;
static KOKKOS_INLINE_FUNCTION
Few<double,3> unmap(Few<double,3> prd, Few<double,6> h, int triclinic,
Few<double,3> x, imageint image);
private:
int groupbit;
double lo[3],hi[3],period[3];
int n_flip, m_flip, p_flip;
ArrayTypes<LMPDeviceType>::t_x_array x;
ArrayTypes<LMPDeviceType>::t_imageint_1d image;
ArrayTypes<LMPDeviceType>::t_int_1d mask;
};
KOKKOS_INLINE_FUNCTION

320
src/KOKKOS/fix_deform_kokkos.cpp
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@ -13,7 +13,8 @@
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
Contributing author: Pieter in 't Veld (SNL)
Contributing author: Pieter in 't Veld (SNL)
Refactoring (2024/08): Mitch Murphy (alphataubio@gmail.com)
------------------------------------------------------------------------- */
#include "fix_deform_kokkos.h"
@ -21,31 +22,14 @@
#include "atom_kokkos.h"
#include "atom_masks.h"
#include "domain_kokkos.h"
#include "force.h"
#include "input.h"
#include "irregular.h"
#include "kspace.h"
#include "math_const.h"
#include "modify.h"
#include "update.h"
#include "variable.h"
#include <cmath>
using namespace LAMMPS_NS;
using namespace FixConst;
using namespace MathConst;
enum{NONE=0,FINAL,DELTA,SCALE,VEL,ERATE,TRATE,VOLUME,WIGGLE,VARIABLE};
enum{ONE_FROM_ONE,ONE_FROM_TWO,TWO_FROM_ONE};
/* ---------------------------------------------------------------------- */
FixDeformKokkos::FixDeformKokkos(LAMMPS *lmp, int narg, char **arg) : FixDeform(lmp, narg, arg)
{
kokkosable = 1;
domainKK = (DomainKokkos *) domain;
datamask_read = EMPTY_MASK;
datamask_modify = EMPTY_MASK;
}
@ -62,308 +46,16 @@ FixDeformKokkos::FixDeformKokkos(LAMMPS *lmp, int narg, char **arg) : FixDeform(
void FixDeformKokkos::pre_exchange()
{
if (flip == 0) return;
domain->yz = set[3].tilt_target = set[3].tilt_flip;
domain->xz = set[4].tilt_target = set[4].tilt_flip;
domain->xy = set[5].tilt_target = set[5].tilt_flip;
domain->set_global_box();
domain->set_local_box();
domainKK->image_flip(flipxy,flipxz,flipyz);
domainKK->remap_all();
domainKK->x2lamda(atom->nlocal);
atomKK->sync(Host,ALL_MASK);
irregular->migrate_atoms();
FixDeform::pre_exchange();
atomKK->modified(Host,ALL_MASK);
domainKK->lamda2x(atom->nlocal);
flip = 0;
}
/* ---------------------------------------------------------------------- */
void FixDeformKokkos::end_of_step()
{
int i;
double delta = update->ntimestep - update->beginstep;
if (delta != 0.0) delta /= update->endstep - update->beginstep;
// wrap variable evaluations with clear/add
if (varflag) modify->clearstep_compute();
// set new box size
// for NONE, target is current box size
// for TRATE, set target directly based on current time, also set h_rate
// for WIGGLE, set target directly based on current time, also set h_rate
// for VARIABLE, set target directly via variable eval, also set h_rate
// for others except VOLUME, target is linear value between start and stop
for (i = 0; i < 3; i++) {
if (set[i].style == NONE) {
set[i].lo_target = domain->boxlo[i];
set[i].hi_target = domain->boxhi[i];
} else if (set[i].style == TRATE) {
double delt = (update->ntimestep - update->beginstep) * update->dt;
set[i].lo_target = 0.5*(set[i].lo_start+set[i].hi_start) -
0.5*((set[i].hi_start-set[i].lo_start) * exp(set[i].rate*delt));
set[i].hi_target = 0.5*(set[i].lo_start+set[i].hi_start) +
0.5*((set[i].hi_start-set[i].lo_start) * exp(set[i].rate*delt));
h_rate[i] = set[i].rate * domain->h[i];
h_ratelo[i] = -0.5*h_rate[i];
} else if (set[i].style == WIGGLE) {
double delt = (update->ntimestep - update->beginstep) * update->dt;
set[i].lo_target = set[i].lo_start -
0.5*set[i].amplitude * sin(MY_2PI*delt/set[i].tperiod);
set[i].hi_target = set[i].hi_start +
0.5*set[i].amplitude * sin(MY_2PI*delt/set[i].tperiod);
h_rate[i] = MY_2PI/set[i].tperiod * set[i].amplitude *
cos(MY_2PI*delt/set[i].tperiod);
h_ratelo[i] = -0.5*h_rate[i];
} else if (set[i].style == VARIABLE) {
double del = input->variable->compute_equal(set[i].hvar);
set[i].lo_target = set[i].lo_start - 0.5*del;
set[i].hi_target = set[i].hi_start + 0.5*del;
h_rate[i] = input->variable->compute_equal(set[i].hratevar);
h_ratelo[i] = -0.5*h_rate[i];
} else if (set[i].style != VOLUME) {
set[i].lo_target = set[i].lo_start +
delta*(set[i].lo_stop - set[i].lo_start);
set[i].hi_target = set[i].hi_start +
delta*(set[i].hi_stop - set[i].hi_start);
}
}
// set new box size for VOLUME dims that are linked to other dims
// NOTE: still need to set h_rate for these dims
for (i = 0; i < 3; i++) {
if (set[i].style != VOLUME) continue;
if (set[i].substyle == ONE_FROM_ONE) {
set[i].lo_target = 0.5*(set[i].lo_start+set[i].hi_start) -
0.5*(set[i].vol_start /
(set[set[i].dynamic1].hi_target -
set[set[i].dynamic1].lo_target) /
(set[set[i].fixed].hi_start-set[set[i].fixed].lo_start));
set[i].hi_target = 0.5*(set[i].lo_start+set[i].hi_start) +
0.5*(set[i].vol_start /
(set[set[i].dynamic1].hi_target -
set[set[i].dynamic1].lo_target) /
(set[set[i].fixed].hi_start-set[set[i].fixed].lo_start));
} else if (set[i].substyle == ONE_FROM_TWO) {
set[i].lo_target = 0.5*(set[i].lo_start+set[i].hi_start) -
0.5*(set[i].vol_start /
(set[set[i].dynamic1].hi_target -
set[set[i].dynamic1].lo_target) /
(set[set[i].dynamic2].hi_target -
set[set[i].dynamic2].lo_target));
set[i].hi_target = 0.5*(set[i].lo_start+set[i].hi_start) +
0.5*(set[i].vol_start /
(set[set[i].dynamic1].hi_target -
set[set[i].dynamic1].lo_target) /
(set[set[i].dynamic2].hi_target -
set[set[i].dynamic2].lo_target));
} else if (set[i].substyle == TWO_FROM_ONE) {
set[i].lo_target = 0.5*(set[i].lo_start+set[i].hi_start) -
0.5*sqrt(set[i].vol_start /
(set[set[i].dynamic1].hi_target -
set[set[i].dynamic1].lo_target) /
(set[set[i].fixed].hi_start -
set[set[i].fixed].lo_start) *
(set[i].hi_start - set[i].lo_start));
set[i].hi_target = 0.5*(set[i].lo_start+set[i].hi_start) +
0.5*sqrt(set[i].vol_start /
(set[set[i].dynamic1].hi_target -
set[set[i].dynamic1].lo_target) /
(set[set[i].fixed].hi_start -
set[set[i].fixed].lo_start) *
(set[i].hi_start - set[i].lo_start));
}
}
// for triclinic, set new box shape
// for NONE, target is current tilt
// for TRATE, set target directly based on current time. also set h_rate
// for WIGGLE, set target directly based on current time. also set h_rate
// for VARIABLE, set target directly via variable eval. also set h_rate
// for other styles, target is linear value between start and stop values
if (triclinic) {
double *h = domain->h;
for (i = 3; i < 6; i++) {
if (set[i].style == NONE) {
if (i == 5) set[i].tilt_target = domain->xy;
else if (i == 4) set[i].tilt_target = domain->xz;
else if (i == 3) set[i].tilt_target = domain->yz;
} else if (set[i].style == TRATE) {
double delt = (update->ntimestep - update->beginstep) * update->dt;
set[i].tilt_target = set[i].tilt_start * exp(set[i].rate*delt);
h_rate[i] = set[i].rate * domain->h[i];
} else if (set[i].style == WIGGLE) {
double delt = (update->ntimestep - update->beginstep) * update->dt;
set[i].tilt_target = set[i].tilt_start +
set[i].amplitude * sin(MY_2PI*delt/set[i].tperiod);
h_rate[i] = MY_2PI/set[i].tperiod * set[i].amplitude *
cos(MY_2PI*delt/set[i].tperiod);
} else if (set[i].style == VARIABLE) {
double delta_tilt = input->variable->compute_equal(set[i].hvar);
set[i].tilt_target = set[i].tilt_start + delta_tilt;
h_rate[i] = input->variable->compute_equal(set[i].hratevar);
} else {
set[i].tilt_target = set[i].tilt_start +
delta*(set[i].tilt_stop - set[i].tilt_start);
}
// tilt_target can be large positive or large negative value
// add/subtract box lengths until tilt_target is closest to current value
int idenom = 0;
if (i == 5) idenom = 0;
else if (i == 4) idenom = 0;
else if (i == 3) idenom = 1;
double denom = set[idenom].hi_target - set[idenom].lo_target;
double current = h[i]/h[idenom];
while (set[i].tilt_target/denom - current > 0.0)
set[i].tilt_target -= denom;
while (set[i].tilt_target/denom - current < 0.0)
set[i].tilt_target += denom;
if (fabs(set[i].tilt_target/denom - 1.0 - current) <
fabs(set[i].tilt_target/denom - current))
set[i].tilt_target -= denom;
}
}
if (varflag) modify->addstep_compute(update->ntimestep + nevery);
// if any tilt ratios exceed 0.5, set flip = 1 and compute new tilt values
// do not flip in x or y if non-periodic (can tilt but not flip)
// this is b/c the box length would be changed (dramatically) by flip
// if yz tilt exceeded, adjust C vector by one B vector
// if xz tilt exceeded, adjust C vector by one A vector
// if xy tilt exceeded, adjust B vector by one A vector
// check yz first since it may change xz, then xz check comes after
// flip is performed on next timestep, before reneighboring in pre-exchange()
if (triclinic && flipflag) {
double xprd = set[0].hi_target - set[0].lo_target;
double yprd = set[1].hi_target - set[1].lo_target;
double xprdinv = 1.0 / xprd;
double yprdinv = 1.0 / yprd;
if (set[3].tilt_target*yprdinv < -0.5 ||
set[3].tilt_target*yprdinv > 0.5 ||
set[4].tilt_target*xprdinv < -0.5 ||
set[4].tilt_target*xprdinv > 0.5 ||
set[5].tilt_target*xprdinv < -0.5 ||
set[5].tilt_target*xprdinv > 0.5) {
set[3].tilt_flip = set[3].tilt_target;
set[4].tilt_flip = set[4].tilt_target;
set[5].tilt_flip = set[5].tilt_target;
flipxy = flipxz = flipyz = 0;
if (domain->yperiodic) {
if (set[3].tilt_flip*yprdinv < -0.5) {
set[3].tilt_flip += yprd;
set[4].tilt_flip += set[5].tilt_flip;
flipyz = 1;
} else if (set[3].tilt_flip*yprdinv > 0.5) {
set[3].tilt_flip -= yprd;
set[4].tilt_flip -= set[5].tilt_flip;
flipyz = -1;
}
}
if (domain->xperiodic) {
if (set[4].tilt_flip*xprdinv < -0.5) {
set[4].tilt_flip += xprd;
flipxz = 1;
}
if (set[4].tilt_flip*xprdinv > 0.5) {
set[4].tilt_flip -= xprd;
flipxz = -1;
}
if (set[5].tilt_flip*xprdinv < -0.5) {
set[5].tilt_flip += xprd;
flipxy = 1;
}
if (set[5].tilt_flip*xprdinv > 0.5) {
set[5].tilt_flip -= xprd;
flipxy = -1;
}
}
flip = 0;
if (flipxy || flipxz || flipyz) flip = 1;
if (flip) next_reneighbor = update->ntimestep + 1;
}
}
// convert atoms and rigid bodies to lamda coords
if (remapflag == Domain::X_REMAP) {
int nlocal = atom->nlocal;
domainKK->x2lamda(nlocal);
if (rfix.size() > 0) {
atomKK->sync(Host,ALL_MASK);
for (auto &ifix : rfix)
ifix->deform(0);
atomKK->modified(Host,ALL_MASK);
}
}
// reset global and local box to new size/shape
// only if deform fix is controlling the dimension
if (set[0].style) {
domain->boxlo[0] = set[0].lo_target;
domain->boxhi[0] = set[0].hi_target;
}
if (set[1].style) {
domain->boxlo[1] = set[1].lo_target;
domain->boxhi[1] = set[1].hi_target;
}
if (set[2].style) {
domain->boxlo[2] = set[2].lo_target;
domain->boxhi[2] = set[2].hi_target;
}
if (triclinic) {
if (set[3].style) domain->yz = set[3].tilt_target;
if (set[4].style) domain->xz = set[4].tilt_target;
if (set[5].style) domain->xy = set[5].tilt_target;
}
domain->set_global_box();
domain->set_local_box();
// convert atoms and rigid bodies back to box coords
if (remapflag == Domain::X_REMAP) {
int nlocal = atom->nlocal;
domainKK->lamda2x(nlocal);
if (rfix.size() > 0) {
atomKK->sync(Host,ALL_MASK);
for (auto &ifix : rfix)
ifix->deform(1);
atomKK->modified(Host,ALL_MASK);
}
}
// redo KSpace coeffs since box has changed
if (kspace_flag) force->kspace->setup();
atomKK->sync(Host,ALL_MASK);
FixDeform::end_of_step();
atomKK->modified(Host,ALL_MASK);
}

4
src/KOKKOS/fix_deform_kokkos.h
View File

@ -34,13 +34,9 @@ class FixDeformKokkos : public FixDeform {
void pre_exchange() override;
void end_of_step() override;
private:
class DomainKokkos *domainKK;
};
}
#endif
#endif

359
src/KOKKOS/fix_efield_kokkos.cpp
View File

@ -13,22 +13,23 @@
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
Contributing author: Trung Nguyen (U Chicago)
Contributing authors: Trung Nguyen (U Chicago)
Mitch Murphy (alphataubio at gmail)
------------------------------------------------------------------------- */
#include "fix_efield_kokkos.h"
#include "atom_kokkos.h"
#include "update.h"
#include "modify.h"
#include "domain_kokkos.h"
#include "region.h"
#include "input.h"
#include "variable.h"
#include "memory_kokkos.h"
#include "error.h"
#include "atom_masks.h"
#include "domain_kokkos.h"
#include "error.h"
#include "input.h"
#include "kokkos_base.h"
#include "memory_kokkos.h"
#include "modify_kokkos.h"
#include "region.h"
#include "update.h"
#include "variable.h"
using namespace LAMMPS_NS;
using namespace FixConst;
@ -44,12 +45,12 @@ FixEfieldKokkos<DeviceType>::FixEfieldKokkos(LAMMPS *lmp, int narg, char **arg)
kokkosable = 1;
atomKK = (AtomKokkos *) atom;
execution_space = ExecutionSpaceFromDevice<DeviceType>::space;
datamask_read = EMPTY_MASK;
datamask_modify = EMPTY_MASK;
datamask_read = X_MASK | F_MASK | TORQUE_MASK | Q_MASK | MU_MASK | IMAGE_MASK | MASK_MASK;
datamask_modify = F_MASK | TORQUE_MASK;
memory->destroy(efield);
memoryKK->create_kokkos(k_efield,efield,maxatom,4,"efield:efield");
d_efield = k_efield.view<DeviceType>();
d_efield = k_efield.template view<DeviceType>();
}
/* ---------------------------------------------------------------------- */
@ -60,7 +61,7 @@ FixEfieldKokkos<DeviceType>::~FixEfieldKokkos()
if (copymode) return;
memoryKK->destroy_kokkos(k_efield,efield);
efield = nullptr;
memoryKK->destroy_kokkos(k_vatom,vatom);
}
/* ---------------------------------------------------------------------- */
@ -77,17 +78,30 @@ void FixEfieldKokkos<DeviceType>::init()
/* ---------------------------------------------------------------------- */
template<class DeviceType>
void FixEfieldKokkos<DeviceType>::post_force(int /*vflag*/)
void FixEfieldKokkos<DeviceType>::post_force(int vflag)
{
atomKK->sync(execution_space, X_MASK | F_MASK | Q_MASK | IMAGE_MASK | MASK_MASK);
atomKK->sync(execution_space, datamask_read);
x = atomKK->k_x.view<DeviceType>();
f = atomKK->k_f.view<DeviceType>();
q = atomKK->k_q.view<DeviceType>();
image = atomKK->k_image.view<DeviceType>();
mask = atomKK->k_mask.view<DeviceType>();
d_x = atomKK->k_x.template view<DeviceType>();
d_f = atomKK->k_f.template view<DeviceType>();
d_q = atomKK->k_q.template view<DeviceType>();
d_mu = atomKK->k_mu.template view<DeviceType>();
d_torque = atomKK->k_torque.template view<DeviceType>();
d_image = atomKK->k_image.template view<DeviceType>();
d_mask = atomKK->k_mask.template view<DeviceType>();
int nlocal = atomKK->nlocal;
int nlocal = atom->nlocal;
// virial setup
v_init(vflag);
// reallocate per-atom arrays if necessary
if (vflag_atom) {
memoryKK->destroy_kokkos(k_vatom,vatom);
memoryKK->create_kokkos(k_vatom,vatom,maxvatom,"efield:vatom");
d_vatom = k_vatom.template view<DeviceType>();
}
// update region if necessary
@ -111,53 +125,24 @@ void FixEfieldKokkos<DeviceType>::post_force(int /*vflag*/)
d_efield = k_efield.view<DeviceType>();
}
fsum[0] = fsum[1] = fsum[2] = fsum[3] = 0.0;
double_4 fsum_kk;
force_flag = 0;
double result[10] = {0.0};
if (varflag == CONSTANT) {
prd = domain->prd;
h = domain->h;
triclinic = domain->triclinic;
copymode = 1;
// It would be more concise to use the operators below, but there is still an issue with unwrap (TODO below)
//Kokkos::parallel_reduce(Kokkos::RangePolicy<DeviceType, TagFixEfieldConstant>(0,nlocal),*this,fsum_kk);
{
// local variables for lambda capture
auto prd = Few<double,3>(domain->prd);
auto h = Few<double,6>(domain->h);
auto triclinic = domain->triclinic;
auto l_ex = ex;
auto l_ey = ey;
auto l_ez = ez;
auto l_x = x;
auto l_q = q;
auto l_f = f;
auto l_mask = mask;
auto l_image = image;
auto l_groupbit = groupbit;
Kokkos::parallel_reduce(nlocal, LAMMPS_LAMBDA(const int& i, double_4& fsum_kk) {
if (l_mask[i] & l_groupbit) {
Few<double,3> x_i;
x_i[0] = l_x(i,0);
x_i[1] = l_x(i,1);
x_i[2] = l_x(i,2);
auto unwrap = DomainKokkos::unmap(prd,h,triclinic,x_i,l_image(i));
auto qtmp = l_q(i);
auto fx = qtmp * l_ex;
auto fy = qtmp * l_ey;
auto fz = qtmp * l_ez;
l_f(i,0) += fx;
l_f(i,1) += fy;
l_f(i,2) += fz;
fsum_kk.d0 -= fx * unwrap[0] + fy * unwrap[1] + fz * unwrap[2];
fsum_kk.d1 += fx;
fsum_kk.d2 += fy;
fsum_kk.d3 += fz;
}
},fsum_kk);
}
if(qflag && muflag)
Kokkos::parallel_reduce(Kokkos::RangePolicy<DeviceType, TagFixEfieldConstant<1,1> >(0,nlocal),*this,result);
else if(qflag && !muflag)
Kokkos::parallel_reduce(Kokkos::RangePolicy<DeviceType, TagFixEfieldConstant<1,0> >(0,nlocal),*this,result);
else if(!qflag && muflag)
Kokkos::parallel_reduce(Kokkos::RangePolicy<DeviceType, TagFixEfieldConstant<0,1> >(0,nlocal),*this,result);
else
Kokkos::parallel_reduce(Kokkos::RangePolicy<DeviceType, TagFixEfieldConstant<0,0> >(0,nlocal),*this,result);
copymode = 0;
@ -167,19 +152,7 @@ void FixEfieldKokkos<DeviceType>::post_force(int /*vflag*/)
atomKK->sync(Host,ALL_MASK); // this can be removed when variable class is ported to Kokkos
modify->clearstep_compute();
if (xstyle == EQUAL) ex = input->variable->compute_equal(xvar);
else if (xstyle == ATOM)
input->variable->compute_atom(xvar,igroup,&efield[0][0],4,0);
if (ystyle == EQUAL) ey = input->variable->compute_equal(yvar);
else if (ystyle == ATOM)
input->variable->compute_atom(yvar,igroup,&efield[0][1],4,0);
if (zstyle == EQUAL) ez = input->variable->compute_equal(zvar);
else if (zstyle == ATOM)
input->variable->compute_atom(zvar,igroup,&efield[0][2],4,0);
modify->addstep_compute(update->ntimestep + 1);
FixEfield::update_efield_variables();
if (varflag == ATOM) { // this can be removed when variable class is ported to Kokkos
k_efield.modify<LMPHostType>();
@ -187,121 +160,154 @@ void FixEfieldKokkos<DeviceType>::post_force(int /*vflag*/)
}
copymode = 1;
// It would be more concise to use the operators below, but there is still an issue with unwrap (TODO below)
//Kokkos::parallel_reduce(Kokkos::RangePolicy<DeviceType, TagFixEfieldNonConstant>(0,nlocal),*this,fsum_kk);
{
// local variables for lambda capture
auto prd = Few<double,3>(domain->prd);
auto h = Few<double,6>(domain->h);
auto triclinic = domain->triclinic;
auto l_ex = ex;
auto l_ey = ey;
auto l_ez = ez;
auto l_d_efield = d_efield;
auto l_x = x;
auto l_q = q;
auto l_f = f;
auto l_mask = mask;
auto l_image = image;
auto l_groupbit = groupbit;
auto l_xstyle = xstyle;
auto l_ystyle = ystyle;
auto l_zstyle = zstyle;
Kokkos::parallel_reduce(nlocal, LAMMPS_LAMBDA(const int& i, double_4& fsum_kk) {
if (l_mask[i] & l_groupbit) {
Few<double,3> x_i;
x_i[0] = l_x(i,0);
x_i[1] = l_x(i,1);
x_i[2] = l_x(i,2);
auto unwrap = DomainKokkos::unmap(prd,h,triclinic,x_i,l_image(i));
auto qtmp = l_q(i);
auto fx = qtmp * l_ex;
auto fy = qtmp * l_ey;
auto fz = qtmp * l_ez;
if (l_xstyle == ATOM) l_f(i,0) += qtmp * l_d_efield(i,0);
else if (l_xstyle) l_f(i,0) += fx;
if (l_ystyle == ATOM) l_f(i,1) += qtmp * l_d_efield(i,1);
else if (l_ystyle) l_f(i,1) += fy;
if (l_zstyle == ATOM) l_f(i,2) += qtmp * l_d_efield(i,2);
else if (l_zstyle) l_f(i,2) += fz;
fsum_kk.d0 -= fx * unwrap[0] + fy * unwrap[1] + fz * unwrap[2];
fsum_kk.d1 += fx;
fsum_kk.d2 += fy;
fsum_kk.d3 += fz;
}
},fsum_kk);
}
if(qflag && muflag)
Kokkos::parallel_reduce(Kokkos::RangePolicy<DeviceType, TagFixEfieldNonConstant<1,1> >(0,nlocal),*this,result);
else if(qflag && !muflag)
Kokkos::parallel_reduce(Kokkos::RangePolicy<DeviceType, TagFixEfieldNonConstant<1,0> >(0,nlocal),*this,result);
else if(!qflag && muflag)
Kokkos::parallel_reduce(Kokkos::RangePolicy<DeviceType, TagFixEfieldNonConstant<0,1> >(0,nlocal),*this,result);
else
Kokkos::parallel_reduce(Kokkos::RangePolicy<DeviceType, TagFixEfieldNonConstant<0,0> >(0,nlocal),*this,result);
copymode = 0;
}
atomKK->modified(execution_space, F_MASK);
atomKK->modified(execution_space, datamask_modify);
fsum[0] = fsum_kk.d0;
fsum[1] = fsum_kk.d1;
fsum[2] = fsum_kk.d2;
fsum[3] = fsum_kk.d3;
}
fsum[0]=result[0];
fsum[1]=result[1];
fsum[2]=result[2];
fsum[3]=result[3];
template<class DeviceType>
KOKKOS_INLINE_FUNCTION
void FixEfieldKokkos<DeviceType>::operator()(TagFixEfieldConstant, const int &i, double_4& fsum_kk) const {
if (mask[i] & groupbit) {
if (region && !d_match[i]) return;
if (vflag_global) {
virial[0] += result[4];
virial[1] += result[5];
virial[2] += result[6];
virial[3] += result[7];
virial[4] += result[8];
virial[5] += result[9];
}
auto prd = Few<double,3>(domain->prd);
auto h = Few<double,6>(domain->h);
auto triclinic = domain->triclinic;
Few<double,3> x_i;
x_i[0] = x(i,0);
x_i[1] = x(i,1);
x_i[2] = x(i,2);
auto unwrap = DomainKokkos::unmap(prd,h,triclinic,x_i,image(i));
const F_FLOAT qtmp = q(i);
const F_FLOAT fx = qtmp * ex;
const F_FLOAT fy = qtmp * ey;
const F_FLOAT fz = qtmp * ez;
f(i,0) += fx;
f(i,1) += fy;
f(i,2) += fz;
// TODO: access to unwrap below crashes
fsum_kk.d0 -= fx * unwrap[0] + fy * unwrap[1] + fz * unwrap[2];
fsum_kk.d1 += fx;
fsum_kk.d2 += fy;
fsum_kk.d3 += fz;
if (vflag_atom) {
k_vatom.template modify<DeviceType>();
k_vatom.template sync<LMPHostType>();
}
}
template<class DeviceType>
template<int QFLAG, int MUFLAG>
KOKKOS_INLINE_FUNCTION
void FixEfieldKokkos<DeviceType>::operator()(TagFixEfieldNonConstant, const int &i, double_4& fsum_kk) const {
auto prd = Few<double,3>(domain->prd);
auto h = Few<double,6>(domain->h);
auto triclinic = domain->triclinic;
if (mask[i] & groupbit) {
void FixEfieldKokkos<DeviceType>::operator()(TagFixEfieldConstant<QFLAG,MUFLAG>, const int &i, value_type result) const {
if ( QFLAG && (d_mask(i) & groupbit)) {
if (region && !d_match[i]) return;
Few<double,3> x_i;
x_i[0] = x(i,0);
x_i[1] = x(i,1);
x_i[2] = x(i,2);
auto unwrap = DomainKokkos::unmap(prd,h,triclinic,x_i,image(i));
const F_FLOAT qtmp = q[i];
const F_FLOAT fx = qtmp * ex;
const F_FLOAT fy = qtmp * ey;
const F_FLOAT fz = qtmp * ez;
if (xstyle == ATOM) f(i,0) += d_efield(i,0);
else if (xstyle) f(i,0) += fx;
if (ystyle == ATOM) f(i,1) += d_efield(i,1);
else if (ystyle) f(i,1) += fy;
if (zstyle == ATOM) f(i,2) += d_efield(i,2);
else if (zstyle) f(i,2) += fz;
// TODO: access to unwrap below crashes
fsum_kk.d0 -= fx * unwrap[0] + fy * unwrap[1] + fz * unwrap[2];
fsum_kk.d1 += fx;
fsum_kk.d2 += fy;
fsum_kk.d3 += fz;
x_i[0] = d_x(i,0);
x_i[1] = d_x(i,1);
x_i[2] = d_x(i,2);
auto unwrapKK = DomainKokkos::unmap(prd,h,triclinic,x_i,d_image(i));
const F_FLOAT fx = d_q(i) * ex;
const F_FLOAT fy = d_q(i) * ey;
const F_FLOAT fz = d_q(i) * ez;
d_f(i,0) += fx;
d_f(i,1) += fy;
d_f(i,2) += fz;
result[0] -= fx * unwrapKK[0] + fy * unwrapKK[1] + fz * unwrapKK[2];
result[1] += fx;
result[2] += fy;
result[3] += fz;
if (evflag) {
double v[6];
v[0] = fx * unwrapKK[0];
v[1] = fy * unwrapKK[1];
v[2] = fz * unwrapKK[2];
v[3] = fx * unwrapKK[1];
v[4] = fx * unwrapKK[2];
v[5] = fy * unwrapKK[2];
v_tally(result, i, v);
}
}
if (MUFLAG && (d_mask(i) & groupbit)) {
if (region && !d_match[i]) return;
d_torque(i,0) += ez * d_mu(i,1) - ey * d_mu(i,2);
d_torque(i,1) += ex * d_mu(i,2) - ez * d_mu(i,0);
d_torque(i,2) += ey * d_mu(i,0) - ex * d_mu(i,1);
result[0] -= d_mu(i,0) * ex + d_mu(i,1) * ey + d_mu(i,2) * ez;
}
}
template<class DeviceType>
template<int QFLAG, int MUFLAG>
KOKKOS_INLINE_FUNCTION
void FixEfieldKokkos<DeviceType>::operator()(TagFixEfieldNonConstant<QFLAG,MUFLAG>, const int &i, value_type result) const {
if ( QFLAG && (d_mask(i) & groupbit)) {
if (region && !d_match[i]) return;
F_FLOAT fx, fy, fz;
if (xstyle == ATOM) fx = qe2f * d_q(i) * d_efield(i,0);
else fx = d_q(i) * ex;
if (ystyle == ATOM) fy = qe2f * d_q(i) * d_efield(i,1);
else fy = d_q(i) * ey;
if (zstyle == ATOM) fz = qe2f * d_q(i) * d_efield(i,2);
else fz = d_q(i) * ez;
d_f(i,0) += fx;
d_f(i,1) += fy;
d_f(i,2) += fz;
result[1] += fx;
result[2] += fy;
result[3] += fz;
if (pstyle == ATOM) result[0] += qe2f * d_q(i) * d_efield(i,3);
else if (estyle == ATOM) result[0] += d_efield(i,3);
}
if (MUFLAG && (d_mask(i) & groupbit)) {
if (region && !d_match[i]) return;
d_torque(i,0) += ez * d_mu(i,1) - ey * d_mu(i,2);
d_torque(i,1) += ex * d_mu(i,2) - ez * d_mu(i,0);
d_torque(i,2) += ey * d_mu(i,0) - ex * d_mu(i,1);
}
}
/* ----------------------------------------------------------------------
tally virial into global and per-atom accumulators
i = local index of atom
v = total virial for the interaction
increment global virial by v
increment per-atom virial by v
this method can be used when fix computes forces in post_force()
and the force depends on a distance to some external object
e.g. fix wall/lj93: compute virial only on owned atoms
------------------------------------------------------------------------- */
template <class DeviceType>
KOKKOS_INLINE_FUNCTION
void FixEfieldKokkos<DeviceType>::v_tally(value_type result, int i, double *v) const
{
if (vflag_global) {
result[4] += v[0];
result[5] += v[1];
result[6] += v[2];
result[7] += v[3];
result[8] += v[4];
result[9] += v[5];
}
if (vflag_atom) {
Kokkos::atomic_add(&(d_vatom(i,0)),v[0]);
Kokkos::atomic_add(&(d_vatom(i,1)),v[1]);
Kokkos::atomic_add(&(d_vatom(i,2)),v[2]);
Kokkos::atomic_add(&(d_vatom(i,3)),v[3]);
Kokkos::atomic_add(&(d_vatom(i,4)),v[4]);
Kokkos::atomic_add(&(d_vatom(i,5)),v[5]);
}
}
@ -311,4 +317,3 @@ template class FixEfieldKokkos<LMPDeviceType>;
template class FixEfieldKokkos<LMPHostType>;
#endif
}

55
src/KOKKOS/fix_efield_kokkos.h
View File

@ -25,35 +25,20 @@ FixStyle(efield/kk/host,FixEfieldKokkos<LMPHostType>);
#include "fix_efield.h"
#include "kokkos_type.h"
#include "kokkos_few.h"
namespace LAMMPS_NS {
struct e_double_4 {
double d0, d1, d2, d3;
KOKKOS_INLINE_FUNCTION
e_double_4() {
d0 = d1 = d2 = d3 = 0.0;
}
KOKKOS_INLINE_FUNCTION
e_double_4& operator+=(const e_double_4 &rhs) {
d0 += rhs.d0;
d1 += rhs.d1;
d2 += rhs.d2;
d3 += rhs.d3;
return *this;
}
};
typedef e_double_4 double_4;
template<int QFLAG, int MUFLAG>
struct TagFixEfieldConstant{};
template<int QFLAG, int MUFLAG>
struct TagFixEfieldNonConstant{};
template<class DeviceType>
class FixEfieldKokkos : public FixEfield {
public:
typedef DeviceType device_type;
typedef double_4 value_type;
typedef ArrayTypes<DeviceType> AT;
FixEfieldKokkos(class LAMMPS *, int, char **);
@ -61,22 +46,40 @@ class FixEfieldKokkos : public FixEfield {
void init() override;
void post_force(int) override;
KOKKOS_INLINE_FUNCTION
void operator()(TagFixEfieldConstant, const int&, double_4&) const;
typedef double value_type[];
const int value_count = 10;
template<int QFLAG, int MUFLAG>
KOKKOS_INLINE_FUNCTION
void operator()(TagFixEfieldNonConstant, const int&, double_4&) const;
void operator()(TagFixEfieldConstant<QFLAG,MUFLAG>, const int&, value_type) const;
template<int QFLAG, int MUFLAG>
KOKKOS_INLINE_FUNCTION
void operator()(TagFixEfieldNonConstant<QFLAG,MUFLAG>, const int&, value_type) const;
private:
DAT::tdual_ffloat_2d k_efield;
typename AT::t_ffloat_2d_randomread d_efield;
typename AT::t_int_1d d_match;
typename AT::t_x_array_randomread x;
typename AT::t_float_1d_randomread q;
typename AT::t_f_array f;
typename AT::t_imageint_1d_randomread image;
typename AT::t_int_1d_randomread mask;
typename AT::t_x_array_randomread d_x;
typename AT::t_float_1d_randomread d_q;
typename AT::t_mu_array_randomread d_mu;
typename AT::t_f_array d_f;
typename AT::t_f_array d_torque;
typename AT::t_imageint_1d_randomread d_image;
typename AT::t_int_1d_randomread d_mask;
Few<double,3> prd;
Few<double,6> h;
int triclinic;
DAT::tdual_virial_array k_vatom;
typename AT::t_virial_array d_vatom;
KOKKOS_INLINE_FUNCTION
void v_tally(value_type, int, double*) const;
};
}

50
src/KOKKOS/fix_nh_kokkos.cpp
View File

@ -13,7 +13,8 @@
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
Contributing author: Stan Moore (SNL)
Contributing authors: Stan Moore (SNL)
Mitch Murphy (alphataubio@gmail.com)
------------------------------------------------------------------------- */
#include "fix_nh_kokkos.h"
@ -37,6 +38,7 @@ using namespace FixConst;
static constexpr double DELTAFLIP = 0.1;
static constexpr double TILTMAX = 1.5;
static constexpr double EPSILON = 1.0e-6;
enum{NOBIAS,BIAS};
enum{NONE,XYZ,XY,YZ,XZ};
@ -50,6 +52,7 @@ template<class DeviceType>
FixNHKokkos<DeviceType>::FixNHKokkos(LAMMPS *lmp, int narg, char **arg) : FixNH(lmp, narg, arg)
{
kokkosable = 1;
atomKK = (AtomKokkos *)atom;
domainKK = (DomainKokkos *) domain;
execution_space = ExecutionSpaceFromDevice<DeviceType>::space;
@ -89,18 +92,21 @@ void FixNHKokkos<DeviceType>::setup(int /*vflag*/)
} else if (pstat_flag) {
// t0 = reference temperature for masses
// set equal to either ptemp or the current temperature
// cannot be done in init() b/c temperature cannot be called there
// is b/c Modify::init() inits computes after fixes due to dof dependence
// guesstimate a unit-dependent t0 if actual T = 0.0
// error if T less than 1e-6
// if it was read in from a restart file, leave it be
if (t0 == 0.0) {
atomKK->sync(temperature->execution_space,temperature->datamask_read);
t0 = temperature->compute_scalar();
atomKK->modified(temperature->execution_space,temperature->datamask_modify);
if (t0 == 0.0) {
if (strcmp(update->unit_style,"lj") == 0) t0 = 1.0;
else t0 = 300.0;
if (p_temp_flag) {
t0 = p_temp;
} else {
atomKK->sync(temperature->execution_space,temperature->datamask_read);
t0 = temperature->compute_scalar();
atomKK->modified(temperature->execution_space,temperature->datamask_modify);
if (t0 < EPSILON)
error->all(FLERR,"Current temperature too close to zero, consider using ptemp keyword");
}
}
t_target = t0;
@ -298,13 +304,14 @@ void FixNHKokkos<DeviceType>::remap()
// convert pertinent atoms and rigid bodies to lamda coords
domainKK->x2lamda(nlocal);
//if (allremap) domainKK->x2lamda(nlocal);
//else {
// for (i = 0; i < nlocal; i++)
// if (mask[i] & dilate_group_bit)
// domain->x2lamda(x[i],x[i]);
//}
x = atomKK->k_x.template view<DeviceType>();
if (allremap) domainKK->x2lamda(nlocal);
else {
for ( int i = 0; i < nlocal; i++)
if (mask[i] & dilate_group_bit)
domainKK->x2lamda(&x(i,0), &x(i,0));
}
if (rfix.size() > 0)
error->all(FLERR,"Cannot (yet) use rigid bodies with fix nh and Kokkos");
@ -446,13 +453,12 @@ void FixNHKokkos<DeviceType>::remap()
// convert pertinent atoms and rigid bodies back to box coords
domainKK->lamda2x(nlocal);
//if (allremap) domainKK->lamda2x(nlocal);
//else {
// for (i = 0; i < nlocal; i++)
// if (mask[i] & dilate_group_bit)
// domain->lamda2x(x[i],x[i]);
//}
if (allremap) domainKK->lamda2x(nlocal);
else {
for ( int i = 0; i < nlocal; i++)
if (mask[i] & dilate_group_bit)
domainKK->lamda2x(&x(i,0), &x(i,0));
}
// for (auto &ifix : rfix) ifix->deform(1);
}

178
src/KOKKOS/fix_wall_lj93_kokkos.cpp
View File

@ -12,11 +12,19 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
Contributing author: Mitch Murphy (alphataubio@gmail.com)
------------------------------------------------------------------------- */
#include "fix_wall_lj93_kokkos.h"
#include "atom_masks.h"
#include "atom_kokkos.h"
#include "error.h"
#include "atom_masks.h"
#include "input.h"
#include "memory_kokkos.h"
#include <iostream>
using namespace LAMMPS_NS;
@ -29,9 +37,91 @@ FixWallLJ93Kokkos<DeviceType>::FixWallLJ93Kokkos(LAMMPS *lmp, int narg, char **a
kokkosable = 1;
atomKK = (AtomKokkos *) atom;
execution_space = ExecutionSpaceFromDevice<DeviceType>::space;
datamask_read = EMPTY_MASK;
datamask_modify = EMPTY_MASK;
virial_global_flag = virial_peratom_flag = 0;
datamask_read = X_MASK | V_MASK | MASK_MASK;
datamask_modify = F_MASK;
memoryKK->create_kokkos(k_cutoff,6,"wall_lj93:cutoff");
memoryKK->create_kokkos(k_coeff1,6,"wall_lj93:coeff1");
memoryKK->create_kokkos(k_coeff2,6,"wall_lj93:coeff2");
memoryKK->create_kokkos(k_coeff3,6,"wall_lj93:coeff3");
memoryKK->create_kokkos(k_coeff4,6,"wall_lj93:coeff4");
memoryKK->create_kokkos(k_offset,6,"wall_lj93:offset");
d_cutoff = k_cutoff.template view<DeviceType>();
d_coeff1 = k_coeff1.template view<DeviceType>();
d_coeff2 = k_coeff2.template view<DeviceType>();
d_coeff3 = k_coeff3.template view<DeviceType>();
d_coeff4 = k_coeff4.template view<DeviceType>();
d_offset = k_offset.template view<DeviceType>();
}
template<class DeviceType>
FixWallLJ93Kokkos<DeviceType>::~FixWallLJ93Kokkos()
{
if (copymode) return;
memoryKK->destroy_kokkos(k_cutoff);
memoryKK->destroy_kokkos(k_coeff1);
memoryKK->destroy_kokkos(k_coeff2);
memoryKK->destroy_kokkos(k_coeff3);
memoryKK->destroy_kokkos(k_coeff4);
memoryKK->destroy_kokkos(k_offset);
memoryKK->destroy_kokkos(k_vatom,vatom);
}
/* ---------------------------------------------------------------------- */
template <class DeviceType>
void FixWallLJ93Kokkos<DeviceType>::precompute(int m)
{
FixWallLJ93::precompute(m);
for( int i=0 ; i<6 ; i++ ) {
k_cutoff.h_view(i) = cutoff[i];
k_coeff1.h_view(i) = coeff1[i];
k_coeff2.h_view(i) = coeff2[i];
k_coeff3.h_view(i) = coeff3[i];
k_coeff4.h_view(i) = coeff4[i];
k_offset.h_view(i) = offset[i];
}
k_cutoff.template modify<LMPHostType>();
k_coeff1.template modify<LMPHostType>();
k_coeff2.template modify<LMPHostType>();
k_coeff3.template modify<LMPHostType>();
k_coeff4.template modify<LMPHostType>();
k_offset.template modify<LMPHostType>();
k_cutoff.template sync<DeviceType>();
k_coeff1.template sync<DeviceType>();
k_coeff2.template sync<DeviceType>();
k_coeff3.template sync<DeviceType>();
k_coeff4.template sync<DeviceType>();
k_offset.template sync<DeviceType>();
}
/* ---------------------------------------------------------------------- */
template <class DeviceType>
void FixWallLJ93Kokkos<DeviceType>::post_force(int vflag)
{
// reallocate per-atom arrays if necessary
if (vflag_atom) {
memoryKK->destroy_kokkos(k_vatom,vatom);
memoryKK->create_kokkos(k_vatom,vatom,maxvatom,"wall_lj93:vatom");
d_vatom = k_vatom.template view<DeviceType>();
}
FixWallLJ93::post_force(vflag);
if (vflag_atom) {
k_vatom.template modify<DeviceType>();
k_vatom.template sync<LMPHostType>();
}
}
/* ----------------------------------------------------------------------
@ -47,47 +137,89 @@ void FixWallLJ93Kokkos<DeviceType>::wall_particle(int m_in, int which, double co
m = m_in;
coord = coord_in;
atomKK->sync(execution_space, X_MASK|F_MASK|MASK_MASK);
x = atomKK->k_x.view<DeviceType>();
f = atomKK->k_f.view<DeviceType>();
mask = atomKK->k_mask.view<DeviceType>();
int nlocal = atom->nlocal;
atomKK->sync(execution_space,datamask_read);
d_x = atomKK->k_x.template view<DeviceType>();
d_f = atomKK->k_f.template view<DeviceType>();
d_mask = atomKK->k_mask.template view<DeviceType>();
int nlocal = atomKK->nlocal;
dim = which / 2;
side = which % 2;
if (side == 0) side = -1;
double result[13] = {0.0};
copymode = 1;
FixWallLJ93KokkosFunctor<DeviceType> wp_functor(this);
Kokkos::parallel_reduce(nlocal,wp_functor,ewall);
Kokkos::parallel_reduce(nlocal,*this,result);
copymode = 0;
atomKK->modified(execution_space, F_MASK);
ewall[0] += result[0];
ewall[m+1] += result[m+1];
atomKK->modified(execution_space,datamask_modify);
if (vflag_global) {
virial[0] += result[7];
virial[1] += result[8];
virial[2] += result[9];
virial[3] += result[10];
virial[4] += result[11];
virial[5] += result[12];
}
}
template <class DeviceType>
KOKKOS_INLINE_FUNCTION
void FixWallLJ93Kokkos<DeviceType>::wall_particle_item(int i, value_type ewall) const {
if (mask(i) & groupbit) {
void FixWallLJ93Kokkos<DeviceType>::operator()(const int &i, value_type result) const {
if (d_mask(i) & groupbit) {
double delta;
if (side < 0) delta = x(i,dim) - coord;
else delta = coord - x(i,dim);
if (delta >= cutoff[m]) return;
if (side < 0) delta = d_x(i,dim) - coord;
else delta = coord - d_x(i,dim);
if (delta >= d_cutoff(m)) return;
if (delta <= 0.0)
Kokkos::abort("Particle on or inside fix wall surface");
double rinv = 1.0/delta;
double r2inv = rinv*rinv;
double r4inv = r2inv*r2inv;
double r10inv = r4inv*r4inv*r2inv;
double fwall = side * (coeff1[m]*r10inv - coeff2[m]*r4inv);
f(i,dim) -= fwall;
ewall[0] += coeff3[m]*r4inv*r4inv*rinv -
coeff4[m]*r2inv*rinv - offset[m];
ewall[m+1] += fwall;
double fwall = side * (d_coeff1(m)*r10inv - d_coeff2(m)*r4inv);
d_f(i,dim) -= fwall;
result[0] += d_coeff3(m)*r4inv*r4inv*rinv - d_coeff4(m)*r2inv*rinv - d_offset(m);
result[m+1] += fwall;
if (evflag) {
double vn;
if (side < 0)
vn = -fwall * delta;
else
vn = fwall * delta;
v_tally(result, dim, i, vn);
}
}
}
/* ----------------------------------------------------------------------
tally virial component into global and per-atom accumulators
n = index of virial component (0-5)
i = local index of atom
vn = nth component of virial for the interaction
increment nth component of global virial by vn
increment nth component of per-atom virial by vn
this method can be used when fix computes forces in post_force()
and the force depends on a distance to some external object
e.g. fix wall/lj93: compute virial only on owned atoms
------------------------------------------------------------------------- */
template <class DeviceType>
KOKKOS_INLINE_FUNCTION
void FixWallLJ93Kokkos<DeviceType>::v_tally(value_type result, int n, int i, double vn) const
{
if (vflag_global)
result[n+7] += vn;
if (vflag_atom)
Kokkos::atomic_add(&(d_vatom(i,n)),vn);
}
namespace LAMMPS_NS {
template class FixWallLJ93Kokkos<LMPDeviceType>;
#ifdef LMP_KOKKOS_GPU

33
src/KOKKOS/fix_wall_lj93_kokkos.h
View File

@ -33,38 +33,37 @@ class FixWallLJ93Kokkos : public FixWallLJ93 {
public:
typedef DeviceType device_type;
typedef ArrayTypes<DeviceType> AT;
typedef double value_type[];
FixWallLJ93Kokkos(class LAMMPS *, int, char **);
~FixWallLJ93Kokkos() override;
void precompute(int) override;
void post_force(int) override;
void wall_particle(int, int, double) override;
int m;
typedef double value_type[];
const int value_count = 13;
KOKKOS_INLINE_FUNCTION
void wall_particle_item(int, value_type) const;
void operator()(const int&, value_type) const;
private:
int dim,side;
double coord;
typename AT::t_x_array x;
typename AT::t_f_array f;
typename AT::t_int_1d mask;
};
typename AT::t_x_array d_x;
typename AT::t_f_array d_f;
typename AT::t_int_1d d_mask;
template <class DeviceType>
struct FixWallLJ93KokkosFunctor {
typedef DeviceType device_type ;
typedef double value_type[];
const int value_count;
DAT::tdual_virial_array k_vatom;
typename AT::t_virial_array d_vatom;
typename AT::tdual_ffloat_1d k_cutoff,k_coeff1,k_coeff2,k_coeff3,k_coeff4,k_offset;
typename AT::t_ffloat_1d d_cutoff,d_coeff1,d_coeff2,d_coeff3,d_coeff4,d_offset;
FixWallLJ93Kokkos<DeviceType> c;
FixWallLJ93KokkosFunctor(FixWallLJ93Kokkos<DeviceType>* c_ptr):
value_count(c_ptr->m+1), c(*c_ptr) {}
KOKKOS_INLINE_FUNCTION
void operator()(const int i, value_type ewall) const {
c.wall_particle_item(i,ewall);
}
void v_tally(value_type, int, int, double) const;
};
}

4
src/KOKKOS/fix_wall_reflect_kokkos.cpp
View File

@ -23,10 +23,6 @@
using namespace LAMMPS_NS;
enum{XLO=0,XHI=1,YLO=2,YHI=3,ZLO=4,ZHI=5};
enum{NONE=0,EDGE,CONSTANT,VARIABLE};
/* ---------------------------------------------------------------------- */
template<class DeviceType>

53
src/domain.cpp
View File

@ -1663,6 +1663,27 @@ void Domain::remap(double *x)
if (triclinic) lamda2x(coord,x);
}
/* ----------------------------------------------------------------------
remap all points into the periodic box no matter how far away
adjust 3 image flags encoded in image accordingly
resulting coord must satisfy lo <= coord < hi
MAX is important since coord - prd < lo can happen when coord = hi
for triclinic, point is converted to lamda coords (0-1) before doing remap
image = 10 bits for each dimension
increment/decrement in wrap-around fashion
------------------------------------------------------------------------- */
void Domain::remap_all()
{
double **x = atom->x;
imageint *image = atom->image;
int nlocal = atom->nlocal;
if (triclinic) x2lamda(nlocal);
for (int i = 0; i < nlocal; i++) remap(x[i],image[i]);
if (triclinic) lamda2x(nlocal);
}
/* ----------------------------------------------------------------------
remap xnew to be within half box length of xold
do it directly, not iteratively, in case is far away
@ -2188,6 +2209,19 @@ void Domain::lamda2x(int n)
}
}
void Domain::lamda2x(int n, int groupbit)
{
double **x = atom->x;
int *mask = atom->mask;
for (int i = 0; i < n; i++)
if (mask[i] & groupbit) {
x[i][0] = h[0]*x[i][0] + h[5]*x[i][1] + h[4]*x[i][2] + boxlo[0];
x[i][1] = h[1]*x[i][1] + h[3]*x[i][2] + boxlo[1];
x[i][2] = h[2]*x[i][2] + boxlo[2];
}
}
/* ----------------------------------------------------------------------
convert box coords to triclinic 0-1 lamda coords for all N atoms
lamda = H^-1 (x - x0)
@ -2209,6 +2243,25 @@ void Domain::x2lamda(int n)
}
}
void Domain::x2lamda(int n, int groupbit)
{
double delta[3];
double **x = atom->x;
int *mask = atom->mask;
for (int i = 0; i < n; i++)
if (mask[i] & groupbit) {
delta[0] = x[i][0] - boxlo[0];
delta[1] = x[i][1] - boxlo[1];
delta[2] = x[i][2] - boxlo[2];
x[i][0] = h_inv[0]*delta[0] + h_inv[5]*delta[1] + h_inv[4]*delta[2];
x[i][1] = h_inv[1]*delta[1] + h_inv[3]*delta[2];
x[i][2] = h_inv[2]*delta[2];
}
}
/* ----------------------------------------------------------------------
convert triclinic 0-1 lamda coords to box coords for one atom
x = H lamda + x0;

3
src/domain.h
View File

@ -136,6 +136,7 @@ class Domain : protected Pointers {
void closest_image(const double *const, const double *const, double *const);
void remap(double *, imageint &);
void remap(double *);
void remap_all();
void remap_near(double *, double *);
void unmap_inv(double *x, imageint);
void unmap(double *, imageint);
@ -166,7 +167,9 @@ class Domain : protected Pointers {
void boundary_string(char *);
virtual void lamda2x(int);
virtual void lamda2x(int, int);
virtual void x2lamda(int);
virtual void x2lamda(int, int);
virtual void lamda2x(double *, double *);
virtual void x2lamda(double *, double *);
int inside(double *);

22
src/fix_deform.cpp
View File

@ -648,11 +648,7 @@ void FixDeform::pre_exchange()
domain->set_local_box();
domain->image_flip(flipxy, flipxz, flipyz);
double **x = atom->x;
imageint *image = atom->image;
int nlocal = atom->nlocal;
for (int i = 0; i < nlocal; i++) domain->remap(x[i],image[i]);
domain->remap_all();
domain->x2lamda(atom->nlocal);
irregular->migrate_atoms();
@ -898,13 +894,7 @@ void FixDeform::update_domain()
// convert atoms and rigid bodies to lamda coords
if (remapflag == Domain::X_REMAP) {
double **x = atom->x;
int *mask = atom->mask;
int nlocal = atom->nlocal;
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit)
domain->x2lamda(x[i], x[i]);
domain->x2lamda(atom->nlocal, groupbit);
for (auto &ifix : rfix)
ifix->deform(0);
@ -937,13 +927,7 @@ void FixDeform::update_domain()
// convert atoms and rigid bodies back to box coords
if (remapflag == Domain::X_REMAP) {
double **x = atom->x;
int *mask = atom->mask;
int nlocal = atom->nlocal;
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit)
domain->lamda2x(x[i], x[i]);
domain->lamda2x(atom->nlocal, groupbit);
for (auto &ifix : rfix)
ifix->deform(1);

1
src/fix_efield.cpp
View File

@ -318,7 +318,6 @@ void FixEfield::post_force(int vflag)
double **x = atom->x;
double fx, fy, fz;
double v[6], unwrap[3];
;
// constant efield

2
src/fix_wall.cpp
View File

@ -27,8 +27,6 @@
using namespace LAMMPS_NS;
using namespace FixConst;
enum { XLO = 0, XHI = 1, YLO = 2, YHI = 3, ZLO = 4, ZHI = 5 };
static const char *wallpos[] = {"xlo", "xhi", "ylo", "yhi", "zlo", "zhi"};
/* ---------------------------------------------------------------------- */

1
src/fix_wall.h
View File

@ -20,6 +20,7 @@ namespace LAMMPS_NS {
class FixWall : public Fix {
public:
enum { XLO = 0, XHI = 1, YLO = 2, YHI = 3, ZLO = 4, ZHI = 5 };
int nwall;
int wallwhich[6];
double coord0[6];

2
unittest/force-styles/test_config.h
View File

@ -70,6 +70,7 @@ public:
std::vector<coord_t> restart_pos;
std::vector<coord_t> run_vel;
std::vector<coord_t> restart_vel;
std::vector<coord_t> run_torque;
TestConfig() :
lammps_version(""), date_generated(""), basename(""), epsilon(1.0e-14), input_file(""),
@ -94,6 +95,7 @@ public:
restart_pos.clear();
run_vel.clear();
restart_vel.clear();
run_torque.clear();
global_vector.clear();
}
TestConfig(const TestConfig &) = delete;

16
unittest/force-styles/test_config_reader.cpp
View File

@ -48,6 +48,7 @@ TestConfigReader::TestConfigReader(TestConfig &config) : config(config)
consumers["run_forces"] = &TestConfigReader::run_forces;
consumers["run_pos"] = &TestConfigReader::run_pos;
consumers["run_vel"] = &TestConfigReader::run_vel;
consumers["run_torque"] = &TestConfigReader::run_torque;
consumers["pair_style"] = &TestConfigReader::pair_style;
consumers["pair_coeff"] = &TestConfigReader::pair_coeff;
@ -228,6 +229,21 @@ void TestConfigReader::run_vel(const yaml_event_t &event)
}
}
void TestConfigReader::run_torque(const yaml_event_t &event)
{
config.run_torque.clear();
config.run_torque.resize(config.natoms + 1);
std::stringstream data((char *)event.data.scalar.value);
std::string line;
while (std::getline(data, line, '\n')) {
int tag;
coord_t xyz;
sscanf(line.c_str(), "%d %lg %lg %lg", &tag, &xyz.x, &xyz.y, &xyz.z);
config.run_torque[tag] = xyz;
}
}
void TestConfigReader::pair_style(const yaml_event_t &event)
{
config.pair_style = (char *)event.data.scalar.value;

1
unittest/force-styles/test_config_reader.h
View File

@ -41,6 +41,7 @@ public:
void run_forces(const yaml_event_t &event);
void run_pos(const yaml_event_t &event);
void run_vel(const yaml_event_t &event);
void run_torque(const yaml_event_t &event);
void pair_style(const yaml_event_t &event);
void pair_coeff(const yaml_event_t &event);
void bond_style(const yaml_event_t &event);

15
unittest/force-styles/test_dihedral_style.cpp
View File

@ -364,7 +364,7 @@ TEST(DihedralStyle, plain)
stats.reset();
auto *icompute = lmp->modify->get_compute_by_id("sum");
double energy = 0.0;
double energy = 0.0;
if (icompute) energy = icompute->compute_scalar();
EXPECT_FP_LE_WITH_EPS(dihedral->energy, test_config.run_energy, epsilon);
EXPECT_FP_LE_WITH_EPS(dihedral->energy, energy, epsilon);
@ -486,7 +486,7 @@ TEST(DihedralStyle, omp)
stats.reset();
auto *icompute = lmp->modify->get_compute_by_id("sum");
double energy = 0.0;
double energy = 0.0;
if (icompute) energy = icompute->compute_scalar();
EXPECT_FP_LE_WITH_EPS(dihedral->energy, test_config.run_energy, epsilon);
// TODO: this is currently broken for OPENMP with dihedral style hybrid
@ -542,8 +542,9 @@ TEST(DihedralStyle, kokkos_omp)
if (test_config.skip_tests.count(test_info_->name())) GTEST_SKIP();
if (!Info::has_accelerator_feature("KOKKOS", "api", "openmp")) GTEST_SKIP();
LAMMPS::argv args = {"DihedralStyle", "-log", "none", "-echo", "screen", "-nocite",
"-k", "on", "t", "4", "-sf", "kk"};
LAMMPS::argv args = {"DihedralStyle", "-log", "none", "-echo", "screen",
"-nocite", "-k", "on", "t", "4",
"-sf", "kk"};
::testing::internal::CaptureStdout();
LAMMPS *lmp = init_lammps(args, test_config, true);
@ -595,9 +596,9 @@ TEST(DihedralStyle, kokkos_omp)
// FIXME: this is currently broken ??? for KOKKOS with dihedral style hybrid
// needs to be fixed in the main code somewhere. Not sure where, though.
//if (test_config.dihedral_style.substr(0, 6) != "hybrid")
// if (test_config.dihedral_style.substr(0, 6) != "hybrid")
// EXPECT_FP_LE_WITH_EPS(dihedral->energy, energy, epsilon);
//if (print_stats) std::cerr << "run_energy stats, newton on: " << stats << std::endl;
// if (print_stats) std::cerr << "run_energy stats, newton on: " << stats << std::endl;
if (!verbose) ::testing::internal::CaptureStdout();
cleanup_lammps(lmp, test_config);
@ -631,7 +632,7 @@ TEST(DihedralStyle, kokkos_omp)
// FIXME: this is currently broken ??? for KOKKOS with dihedral style hybrid
// needs to be fixed in the main code somewhere. Not sure where, though.
//if (test_config.dihedral_style.substr(0, 6) != "hybrid")
// if (test_config.dihedral_style.substr(0, 6) != "hybrid")
// EXPECT_FP_LE_WITH_EPS(dihedral->energy, energy, epsilon);
if (print_stats) std::cerr << "run_energy stats, newton off:" << stats << std::endl;

193
unittest/force-styles/test_fix_timestep.cpp
View File

@ -244,6 +244,20 @@ void generate_yaml_file(const char *outfile, const TestConfig &config)
block += fmt::format("{:3} {:23.16e} {:23.16e} {:23.16e}\n", i, v[j][0], v[j][1], v[j][2]);
}
writer.emit_block("run_vel", block);
// run_torque
if (lmp->atom->torque_flag) {
block.clear();
auto *t = lmp->atom->torque;
for (int i = 1; i <= natoms; ++i) {
const int j = lmp->atom->map(i);
block +=
fmt::format("{:3} {:23.16e} {:23.16e} {:23.16e}\n", i, t[j][0], t[j][1], t[j][2]);
}
writer.emit_block("run_torque", block);
}
cleanup_lammps(lmp, config);
}
@ -288,6 +302,9 @@ TEST(FixTimestep, plain)
EXPECT_POSITIONS("run_pos (normal run, verlet)", lmp->atom, test_config.run_pos, epsilon);
EXPECT_VELOCITIES("run_vel (normal run, verlet)", lmp->atom, test_config.run_vel, epsilon);
if (lmp->atom->torque_flag)
EXPECT_TORQUES("run_torques (normal run, verlet)", lmp->atom, test_config.run_torque,
epsilon);
auto *ifix = lmp->modify->get_fix_by_id("test");
if (!ifix) {
@ -337,6 +354,8 @@ TEST(FixTimestep, plain)
EXPECT_POSITIONS("run_pos (restart, verlet)", lmp->atom, test_config.run_pos, epsilon);
EXPECT_VELOCITIES("run_vel (restart, verlet)", lmp->atom, test_config.run_vel, epsilon);
if (lmp->atom->torque_flag)
EXPECT_TORQUES("run_torque (restart, verlet)", lmp->atom, test_config.run_torque, epsilon);
ifix = lmp->modify->get_fix_by_id("test");
if (!ifix) {
@ -832,3 +851,177 @@ TEST(FixTimestep, omp)
cleanup_lammps(lmp, test_config);
if (!verbose) ::testing::internal::GetCapturedStdout();
};
TEST(FixTimestep, kokkos_omp)
{
if (!LAMMPS::is_installed_pkg("KOKKOS")) GTEST_SKIP();
if (test_config.skip_tests.count(test_info_->name())) GTEST_SKIP();
if (!Info::has_accelerator_feature("KOKKOS", "api", "openmp")) GTEST_SKIP();
LAMMPS::argv args = {"FixTimestep", "-log", "none", "-echo", "screen", "-nocite",
"-k", "on", "t", "4", "-sf", "kk"};
::testing::internal::CaptureStdout();
LAMMPS *lmp = init_lammps(args, test_config);
std::string output = ::testing::internal::GetCapturedStdout();
if (verbose) std::cout << output;
if (!lmp) {
std::cerr << "One or more prerequisite styles with /kk suffix\n"
"are not available in this LAMMPS configuration:\n";
for (auto &prerequisite : test_config.prerequisites) {
std::cerr << prerequisite.first << "_style " << prerequisite.second << "\n";
}
GTEST_SKIP();
}
EXPECT_THAT(output, StartsWith("LAMMPS ("));
EXPECT_THAT(output, HasSubstr("Loop time"));
// abort if running in parallel and not all atoms are local
const int nlocal = lmp->atom->nlocal;
ASSERT_EQ(lmp->atom->natoms, nlocal);
// relax error a bit for KOKKOS package
double epsilon = 10.0 * test_config.epsilon;
// relax test precision when using pppm and single precision FFTs
#if defined(FFT_SINGLE)
if (lmp->force->kspace && utils::strmatch(lmp->force->kspace_style, "^pppm")) epsilon *= 2.0e8;
#endif
ErrorStats stats;
EXPECT_POSITIONS("run_pos (normal run, verlet)", lmp->atom, test_config.run_pos, epsilon);
EXPECT_VELOCITIES("run_vel (normal run, verlet)", lmp->atom, test_config.run_vel, epsilon);
if (lmp->atom->torque_flag)
EXPECT_TORQUES("run_torque (normal run, verlet)", lmp->atom, test_config.run_torque,
epsilon);
auto *ifix = lmp->modify->get_fix_by_id("test");
if (!ifix) {
FAIL() << "ERROR: no fix defined with fix ID 'test'\n";
} else {
if (ifix->thermo_virial) {
EXPECT_STRESS("run_stress (normal run, verlet)", ifix->virial, test_config.run_stress,
epsilon);
}
stats.reset();
// global scalar
if (ifix->scalar_flag) {
double value = ifix->compute_scalar();
EXPECT_FP_LE_WITH_EPS(test_config.global_scalar, value, epsilon);
}
// global vector
if (ifix->vector_flag) {
int num = ifix->size_vector;
EXPECT_EQ(num, test_config.global_vector.size());
for (int i = 0; i < num; ++i)
EXPECT_FP_LE_WITH_EPS(test_config.global_vector[i], ifix->compute_vector(i),
epsilon);
}
// check t_target for thermostats
int dim = -1;
double *ptr = (double *)ifix->extract("t_target", dim);
if ((ptr != nullptr) && (dim == 0)) {
int ivar = lmp->input->variable->find("t_target");
if (ivar >= 0) {
double t_ref = atof(lmp->input->variable->retrieve("t_target"));
double t_target = *ptr;
EXPECT_FP_LE_WITH_EPS(t_target, t_ref, epsilon);
}
}
if (print_stats && stats.has_data())
std::cerr << "global_data, normal run, verlet: " << stats << std::endl;
}
if (!verbose) ::testing::internal::CaptureStdout();
restart_lammps(lmp, test_config, false, false);
if (!verbose) ::testing::internal::GetCapturedStdout();
EXPECT_POSITIONS("run_pos (restart, verlet)", lmp->atom, test_config.run_pos, epsilon);
EXPECT_VELOCITIES("run_vel (restart, verlet)", lmp->atom, test_config.run_vel, epsilon);
if (lmp->atom->torque_flag)
EXPECT_TORQUES("run_torque (restart, verlet)", lmp->atom, test_config.run_torque, epsilon);
ifix = lmp->modify->get_fix_by_id("test");
if (!ifix) {
FAIL() << "ERROR: no fix defined with fix ID 'test'\n";
} else {
if (ifix->thermo_virial) {
EXPECT_STRESS("run_stress (restart, verlet)", ifix->virial, test_config.run_stress,
epsilon);
}
stats.reset();
// global scalar
if (ifix->scalar_flag) {
double value = ifix->compute_scalar();
EXPECT_FP_LE_WITH_EPS(test_config.global_scalar, value, epsilon);
}
// global vector
if (ifix->vector_flag) {
int num = ifix->size_vector;
EXPECT_EQ(num, test_config.global_vector.size());
for (int i = 0; i < num; ++i)
EXPECT_FP_LE_WITH_EPS(test_config.global_vector[i], ifix->compute_vector(i),
epsilon);
}
if (print_stats && stats.has_data())
std::cerr << "global_data, restart, verlet: " << stats << std::endl;
}
if (lmp->atom->rmass == nullptr) {
if (!verbose) ::testing::internal::CaptureStdout();
restart_lammps(lmp, test_config, true, false);
if (!verbose) ::testing::internal::GetCapturedStdout();
EXPECT_POSITIONS("run_pos (rmass, verlet)", lmp->atom, test_config.run_pos, epsilon);
EXPECT_VELOCITIES("run_vel (rmass, verlet)", lmp->atom, test_config.run_vel, epsilon);
ifix = lmp->modify->get_fix_by_id("test");
if (!ifix) {
FAIL() << "ERROR: no fix defined with fix ID 'test'\n";
} else {
if (ifix->thermo_virial) {
EXPECT_STRESS("run_stress (rmass, verlet)", ifix->virial, test_config.run_stress,
epsilon);
}
stats.reset();
// global scalar
if (ifix->scalar_flag) {
double value = ifix->compute_scalar();
EXPECT_FP_LE_WITH_EPS(test_config.global_scalar, value, epsilon);
}
// global vector
if (ifix->vector_flag) {
int num = ifix->size_vector;
EXPECT_EQ(num, test_config.global_vector.size());
for (int i = 0; i < num; ++i)
EXPECT_FP_LE_WITH_EPS(test_config.global_vector[i], ifix->compute_vector(i),
epsilon);
}
if (print_stats && stats.has_data())
std::cerr << "global_data, rmass, verlet: " << stats << std::endl;
}
}
// skip RESPA tests for KOKKOS
if (!verbose) ::testing::internal::CaptureStdout();
cleanup_lammps(lmp, test_config);
if (!verbose) ::testing::internal::GetCapturedStdout();
};

17
unittest/force-styles/test_main.cpp
View File

@ -101,6 +101,23 @@ void EXPECT_VELOCITIES(const std::string &name, Atom *atom, const std::vector<co
if (print_stats) std::cerr << name << " stats: " << stats << std::endl;
}
void EXPECT_TORQUES(const std::string &name, Atom *atom, const std::vector<coord_t> &t_ref,
double epsilon)
{
SCOPED_TRACE("EXPECT_TORQUES: " + name);
double **t = atom->torque;
tagint *tag = atom->tag;
const int nlocal = atom->nlocal;
ASSERT_EQ(nlocal + 1, t_ref.size());
ErrorStats stats;
for (int i = 0; i < nlocal; ++i) {
EXPECT_FP_LE_WITH_EPS(t[i][0], t_ref[tag[i]].x, epsilon);
EXPECT_FP_LE_WITH_EPS(t[i][1], t_ref[tag[i]].y, epsilon);
EXPECT_FP_LE_WITH_EPS(t[i][2], t_ref[tag[i]].z, epsilon);
}
if (print_stats) std::cerr << name << " stats: " << stats << std::endl;
}
// common read_yaml_file function
bool read_yaml_file(const char *infile, TestConfig &config)
{

2
unittest/force-styles/test_main.h
View File

@ -45,5 +45,7 @@ void EXPECT_POSITIONS(const std::string &name, LAMMPS_NS::Atom *atom,
const std::vector<coord_t> &x_ref, double epsilon);
void EXPECT_VELOCITIES(const std::string &name, LAMMPS_NS::Atom *atom,
const std::vector<coord_t> &v_ref, double epsilon);
void EXPECT_TORQUES(const std::string &name, LAMMPS_NS::Atom *atom,
const std::vector<coord_t> &t_ref, double epsilon);
#endif

58
unittest/force-styles/tests/fix-timestep-efield_const.yaml
View File

@ -1,6 +1,7 @@
---
lammps_version: 17 Feb 2022
date_generated: Fri Mar 18 22:17:58 2022
lammps_version: 27 Jun 2024
tags: generated
date_generated: Tue Aug 6 02:04:43 2024
epsilon: 2e-13
skip_tests:
prerequisites: ! |
@ -10,11 +11,14 @@ pre_commands: ! ""
post_commands: ! |
fix move all nve
fix test solute efield 0.0 -0.1 0.1
fix_modify test virial yes
input_file: in.fourmol
natoms: 29
run_stress: ! |2-
0.0000000000000000e+00 3.1221533030312409e-01 -2.8129669718847106e-01 0.0000000000000000e+00 0.0000000000000000e+00 2.8129669718847106e-01
global_scalar: -0.030918633114652927
global_vector: ! |-
3 0 -2.220446049250313e-16 2.220446049250313e-16
3 0 0 0
run_pos: ! |2
1 -2.7045797446143222e-01 2.4912780824342802e+00 -1.6702148063946790e-01
2 3.1004707684044314e-01 2.9610914097014920e+00 -8.5452223796947857e-01
@ -46,33 +50,33 @@ run_pos: ! |2
28 -2.7473562684513779e+00 -4.0200819932379650e+00 1.5830052163433976e+00
29 -1.3126000191359843e+00 -3.5962518039484861e+00 2.2746342468738585e+00
run_vel: ! |2
1 8.1658312222614663e-03 1.6575957150422167e-02 4.7291974403202448e-03
2 5.4638876708023821e-03 5.0404029111476506e-03 -1.3039774181753307e-03
3 -8.2285460105815302e-03 -1.2921801247052923e-02 -4.0992611431015756e-03
4 -3.7708744841912487e-03 -6.6156123307326833e-03 -1.0763844399678132e-03
5 -1.1020911952034354e-02 -9.9319392840069663e-03 -2.7996700321696274e-03
1 8.1658312222614663e-03 1.6575957150422167e-02 4.7291974403202422e-03
2 5.4638876708023821e-03 5.0404029111476524e-03 -1.3039774181753297e-03
3 -8.2285460105815285e-03 -1.2921801247052927e-02 -4.0992611431015730e-03
4 -3.7708744841912487e-03 -6.6156123307326850e-03 -1.0763844399678134e-03
5 -1.1020911952034355e-02 -9.9319392840069645e-03 -2.7996700321696287e-03
6 -3.9693502572798259e-02 4.6742328405570736e-02 3.7202597389078947e-02
7 9.0976114937484250e-04 -1.0062942346953162e-02 -5.1616508395410758e-02
8 7.9254327404120941e-03 -3.2975389442540595e-03 3.4504402492869846e-02
9 1.5591017009909064e-03 3.5830453659612422e-03 1.5180501660659096e-02
7 9.0976114937484228e-04 -1.0062942346953162e-02 -5.1616508395410758e-02
8 7.9254327404120941e-03 -3.2975389442540604e-03 3.4504402492869859e-02
9 1.5591017009909053e-03 3.5830453659612426e-03 1.5180501660659096e-02
10 2.9199490526855283e-02 -2.9258641689434338e-02 -1.5005297297757594e-02
11 -4.7836605087433386e-03 -3.7914729059920198e-03 -2.3035595838662840e-03
12 2.2697954637435859e-03 -3.0717924023358485e-04 -3.1050775042142892e-03
13 2.7523035532740596e-03 5.7750272572237955e-03 -7.5235664623991166e-04
14 3.5240740939544214e-03 -5.8353371764581791e-03 -3.9081837862824593e-03
11 -4.7836605087433395e-03 -3.7914729059920194e-03 -2.3035595838662840e-03
12 2.2697954637435872e-03 -3.0717924023358680e-04 -3.1050775042142913e-03
13 2.7523035532740596e-03 5.7750272572237955e-03 -7.5235664623990917e-04
14 3.5240740939544192e-03 -5.8353371764581765e-03 -3.9081837862824575e-03
15 -1.8549049501666087e-03 -5.8961708769767604e-03 6.3361117899020467e-03
16 1.8685917131732017e-02 -1.3347834929626302e-02 -4.5570644533488594e-02
17 -1.2900152726318757e-02 9.8178161596953993e-03 3.7244993882472807e-02
18 -8.0065793345388101e-04 -8.6270471230818341e-04 -1.4483040707563421e-03
19 1.2452390842995829e-03 -2.5061097113172779e-03 7.2998631014686054e-03
20 3.5930060230102141e-03 3.6938860309017889e-03 3.2322732690523012e-03
21 -1.4689220346471620e-03 -2.7352130047668410e-04 7.0581623957410638e-04
22 -7.0694199254063778e-03 -4.2577148925930248e-03 2.8079117595076618e-04
23 6.0446963119010697e-03 -1.4000131615444645e-03 2.5819754845290274e-03
24 3.1926368357822996e-04 -9.9445664356196447e-04 1.4999997179198298e-04
25 1.3789755154241975e-04 -4.4335894822910855e-03 -8.1808135929846665e-04
26 2.0485904038928891e-03 2.7813358638196055e-03 4.3245727151208667e-03
27 4.5604119916965464e-04 -1.0305523051824380e-03 2.1188058452236590e-04
28 -6.2544520862769975e-03 1.4127711175481057e-03 -1.8429821884839938e-03
29 6.4110631531126019e-04 3.1273432715248138e-03 3.7253671107199712e-03
18 -8.0065793345388101e-04 -8.6270471230818330e-04 -1.4483040707563431e-03
19 1.2452390842995818e-03 -2.5061097113172792e-03 7.2998631014686071e-03
20 3.5930060230102141e-03 3.6938860309017889e-03 3.2322732690523034e-03
21 -1.4689220346471620e-03 -2.7352130047668405e-04 7.0581623957410638e-04
22 -7.0694199254063787e-03 -4.2577148925930248e-03 2.8079117595076618e-04
23 6.0446963119010697e-03 -1.4000131615444645e-03 2.5819754845290278e-03
24 3.1926368357822991e-04 -9.9445664356196447e-04 1.4999997179198287e-04
25 1.3789755154241959e-04 -4.4335894822910855e-03 -8.1808135929846654e-04
26 2.0485904038928895e-03 2.7813358638196051e-03 4.3245727151208667e-03
27 4.5604119916965442e-04 -1.0305523051824363e-03 2.1188058452236553e-04
28 -6.2544520862769983e-03 1.4127711175481021e-03 -1.8429821884839938e-03
29 6.4110631531126225e-04 3.1273432715248112e-03 3.7253671107199729e-03
...

109
unittest/force-styles/tests/fix-timestep-efield_dipole_const.yaml Normal file
View File

@ -0,0 +1,109 @@
---
lammps_version: 27 Jun 2024
tags: generated
date_generated: Sun Aug 4 21:46:33 2024
epsilon: 2e-13
skip_tests:
prerequisites: ! |
atom full
fix efield
pre_commands: ! ""
post_commands: ! |
fix move all nve
fix test solute efield 0.0 -0.1 0.1
input_file: in.dipole
natoms: 29
global_scalar: 5.323551487649474
global_vector: ! |-
3 0 0 0
run_pos: ! |2
1 -2.7803395919988250e-01 2.4746113957575506e+00 -1.7221055624989043e-01
2 3.0862275733044281e-01 2.9608256711658929e+00 -8.5204259894833823e-01
3 -6.9730353651054677e-01 1.2462185235506165e+00 -6.2333170008106076e-01
4 -1.5803707788642558e+00 1.4864216493511191e+00 -1.2553333144872691e+00
5 -9.0224637486770010e-01 9.3187101763772007e-01 4.0100026498818492e-01
6 2.9068098249777818e-01 2.3317755418235958e-01 -1.2787854346401060e+00
7 3.4003718022438006e-01 -1.1136458545317439e-02 -2.4674043539784920e+00
8 1.1653603994058781e+00 -4.8553538245393735e-01 -6.7455699042973893e-01
9 1.3798605257891061e+00 -2.5606949147401714e-01 2.7646698442033224e-01
10 2.0213511597812359e+00 -1.4294263001051324e+00 -9.6869511230628547e-01
11 1.7900398780219073e+00 -1.9910605295844079e+00 -1.8892677004539045e+00
12 3.0052519569684715e+00 -4.9050496445328290e-01 -1.6215568178297506e+00
13 4.0521826738629381e+00 -8.9321351964942697e-01 -1.6399622114060945e+00
14 2.6048704355881833e+00 -4.1699645854738832e-01 -2.6633172811775432e+00
15 2.9682789927413045e+00 5.5558820658819164e-01 -1.2357788915285541e+00
16 2.6531499373970879e+00 -2.3977947524956051e+00 3.1767580086883969e-02
17 2.2316478624956817e+00 -2.1010963925555934e+00 1.1526347069081506e+00
18 2.1372510164775917e+00 3.0158506000670471e+00 -3.5167916423912540e+00
19 1.5345707099325703e+00 2.6249696297497245e+00 -4.2370263294605586e+00
20 2.7732095850735732e+00 3.6929598470822609e+00 -3.9337745509644702e+00
21 4.9045170966506779e+00 -4.0748031756039733e+00 -3.6218925414637724e+00
22 4.3601484254173615e+00 -4.2118940901718647e+00 -4.4596265759840623e+00
23 5.7410255603426821e+00 -3.5837707365543663e+00 -3.8765903698198994e+00
24 2.0689205181437282e+00 3.1527432700151787e+00 3.1544823899087238e+00
25 1.3065187961786864e+00 3.2665243034421700e+00 2.5127268092211676e+00
26 2.5789541569135683e+00 4.0089379439900057e+00 3.2207820820981503e+00
27 -1.9618638791883916e+00 -4.3549504053758268e+00 2.1090482240812847e+00
28 -2.7443201293863742e+00 -4.0212170735729584e+00 1.5850082667482344e+00
29 -1.3141860113747614e+00 -3.5978986954166352e+00 2.2741894687371453e+00
run_vel: ! |2
1 1.1236143544142998e-03 1.3615061488813968e-03 1.9035146531107875e-05
2 3.8968322106659220e-03 4.6153851102938084e-03 1.3004266866309365e-03
3 -1.6759039090575756e-03 5.6410326296895460e-04 -6.5573998085605308e-04
4 -2.2599843514772115e-03 -3.8290476239094783e-03 -2.4796763793128265e-03
5 -6.0394625433784410e-03 -4.5348465561185066e-03 -1.3711951052336872e-03
6 -3.1023884715655490e-03 4.6637296517233725e-03 4.6189123645965016e-03
7 -5.2419935748452737e-05 -1.2319086507260619e-03 -3.2654613259055676e-03
8 8.3601735362959304e-04 -9.5637212087811387e-04 1.8785968961167793e-03
9 8.4122759994834529e-04 2.0922433389435784e-04 6.4346601850387691e-03
10 2.3678265535346989e-03 -1.5212081023084892e-03 -1.1281854658615922e-03
11 -2.5475261615126705e-03 -2.3919533481450207e-03 -2.2311276418214019e-03
12 1.1421771336981225e-03 -6.2449989986439278e-04 -1.3944269209182573e-03
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18 -6.1590009973258066e-04 -9.3553764271450690e-04 -3.7200153139999693e-04
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29 -8.6242002778640222e-04 1.5767896868750036e-03 3.2980383776088458e-03
run_torque: ! |2
1 -8.5357527435914071e-01 -5.3719824654427417e-01 -5.3719824654427417e-01
2 1.1164762300859654e+00 1.0884510402842875e+00 1.0884510402842875e+00
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8 -1.1874337657028966e+00 -2.6646753617169627e-01 -2.6646753617169627e-01
9 -1.0177972619106430e+00 2.1477723017368913e+00 2.1477723017368913e+00
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11 -1.3439139083704066e+00 1.5074058265158885e+00 1.5074058265158885e+00
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...

118
unittest/force-styles/tests/fix-timestep-efield_dipole_variable.yaml Normal file
View File

@ -0,0 +1,118 @@
---
lammps_version: 27 Jun 2024
tags: generated
date_generated: Sun Aug 4 22:46:18 2024
epsilon: 2e-13
skip_tests:
prerequisites: ! |
atom full
fix efield
pre_commands: ! ""
post_commands: ! |
fix move all nve
variable xforce delete
variable xforce equal 0.1*step/10.0
variable yforce delete
variable yforce equal 0.2*step/20.0
variable zforce delete
variable zforce equal 0.3*step/30.0
fix test solute efield v_xforce v_yforce v_zforce
fix_modify test virial yes
input_file: in.dipole
natoms: 29
run_stress: ! |2-
0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
global_scalar: 0
global_vector: ! |-
3 -1.1102230246251565e-16 -1.1102230246251565e-16 -1.1102230246251565e-16
run_pos: ! |2
1 -2.7803462088205888e-01 2.4746080899361873e+00 -1.7220863968422631e-01
2 3.0864099030230185e-01 2.9609184454137019e+00 -8.5209600355138704e-01
3 -6.9730358393070480e-01 1.2462183036890040e+00 -6.2333158600291183e-01
4 -1.5803650460394709e+00 1.4864488193383358e+00 -1.2553491245822981e+00
5 -9.0224083555581314e-01 9.3189811105149611e-01 4.0098458630849332e-01
6 2.9068221058927873e-01 2.3318328040718064e-01 -1.2787887242994260e+00
7 3.4003667591250708e-01 -1.1138891887048934e-02 -2.4674029540393323e+00
8 1.1653596712202525e+00 -4.8553870127449805e-01 -6.7455507659928038e-01
9 1.3798803918386071e+00 -2.5597543756832153e-01 2.7641311417048842e-01
10 2.0213513284917770e+00 -1.4294255167846066e+00 -9.6869557537003070e-01
11 1.7900455523978396e+00 -1.9910333303206023e+00 -1.8892835721159780e+00
12 3.0052513251780613e+00 -4.9050798224436865e-01 -1.6215550550329203e+00
13 4.0521883707492767e+00 -8.9318637207253593e-01 -1.6399780787400113e+00
14 2.6048761179356523e+00 -4.1696935840940191e-01 -2.6633329891570114e+00
15 2.9682846368976175e+00 5.5561522368460747e-01 -1.2357947529810707e+00
16 2.6531511203883147e+00 -2.3977890057416973e+00 3.1764256827161913e-02
17 2.2316473623837325e+00 -2.1010988247185729e+00 1.1526361129941032e+00
18 2.1372510164775789e+00 3.0158506000670355e+00 -3.5167916423912531e+00
19 1.5345707099325570e+00 2.6249696297497045e+00 -4.2370263294605177e+00
20 2.7732095850735634e+00 3.6929598470822547e+00 -3.9337745509644595e+00
21 4.9045170966506770e+00 -4.0748031756039724e+00 -3.6218925414637728e+00
22 4.3601484254173615e+00 -4.2118940901718629e+00 -4.4596265759840614e+00
23 5.7410255603426812e+00 -3.5837707365543650e+00 -3.8765903698198989e+00
24 2.0689205181437282e+00 3.1527432700151770e+00 3.1544823899087251e+00
25 1.3065187961786540e+00 3.2665243034421243e+00 2.5127268092211485e+00
26 2.5789541569135679e+00 4.0089379439900039e+00 3.2207820820981503e+00
27 -1.9618638791883911e+00 -4.3549504053758268e+00 2.1090482240812847e+00
28 -2.7443201293863759e+00 -4.0212170735729593e+00 1.5850082667482348e+00
29 -1.3141860113747683e+00 -3.5978986954166383e+00 2.2741894687371484e+00
run_vel: ! |2
1 1.1226228998813120e-03 1.3578676832028912e-03 2.0557170947250780e-05
2 3.9239288756989016e-03 4.7172177954433788e-03 1.2587212580222184e-03
3 -1.6759752389904064e-03 5.6386389592282232e-04 -6.5566849439663093e-04
4 -2.2512384997042472e-03 -3.7989938232970300e-03 -2.4924216203737527e-03
5 -6.0310935807221877e-03 -4.5049478412039637e-03 -1.3836695500793908e-03
6 -3.1005005132647293e-03 4.6700701138933255e-03 4.6163000387542787e-03
7 -5.3188586817768639e-05 -1.2346121248938561e-03 -3.2643401792630212e-03
8 8.3489219083866242e-04 -9.6003848332027136e-04 1.8801202990819514e-03
9 8.7162816848026234e-04 3.1364623622102896e-04 6.3917296813706522e-03
10 2.3680868557455818e-03 -1.5203429248592441e-03 -1.1285650316897892e-03
11 -2.5388840283489342e-03 -2.3618541252316532e-03 -2.2440122087485034e-03
12 1.1412159144708132e-03 -6.2782650780501229e-04 -1.3930048293318753e-03
13 3.3658569001843641e-03 4.6217055285812667e-03 -7.3566554681633899e-04
14 1.7149215410627553e-03 -4.9542364152862740e-03 -3.8999231155933270e-03
15 -3.0204251503176452e-03 -4.5033742607606102e-03 4.7230261700345021e-03
16 1.4757444573234482e-03 -1.5666516321294532e-03 -2.5937088506404159e-03
17 1.0571264012818976e-06 8.2201760099452344e-04 2.5872403829922935e-03
18 -6.1590009975964484e-04 -9.3553764274130838e-04 -3.7200153139700973e-04
19 3.2061425507972274e-04 -3.0287047641009905e-03 5.8636911224663182e-03
20 4.1715098782492523e-03 4.3790563537376538e-03 2.5400818877933480e-03
21 -9.7312009033487896e-04 1.5100049673665020e-04 -1.5172282348215765e-04
22 -5.2572212429864151e-03 -3.5787417430601385e-03 1.8543943930504219e-03
23 3.2939362683093013e-03 -2.8836279185044679e-03 2.6255213558361900e-03
24 2.5638398658362307e-04 4.3450813156448382e-04 -4.5928187144820296e-04
25 2.1619084723496903e-03 -4.4534715376318085e-03 7.6930725246239842e-04
26 1.6282501420679502e-04 5.6085644857617055e-05 3.9231484240590028e-03
27 -2.4066098679621984e-04 3.1636377958145940e-04 -5.3626843391455024e-04
28 -3.4277217399801899e-03 3.7010237059051832e-04 1.5959546006432193e-05
29 -8.6242002780014568e-04 1.5767896868705918e-03 3.2980383776149932e-03
run_torque: ! |2
1 -2.4436070050579253e+00 4.5061479554988704e-01 1.9929922095080381e+00
2 2.1195936058917191e+00 2.5755452131595669e-01 -2.3771481272076755e+00
3 -2.5250330905076650e+00 1.7960867151270548e+00 7.2894637538061047e-01
4 -8.3457683612426237e-01 2.1064060533126194e+00 -1.2718292171883570e+00
5 1.7827105075374519e+00 -1.0429633292471694e+00 -7.3974717829028225e-01
6 2.4804444324082988e+00 -9.8252359215704177e-01 -1.4979208402512567e+00
7 2.1855709506971714e+00 -2.2850183382383915e+00 9.9447387541219956e-02
8 2.4111434047810372e+00 -1.8937192376090342e+00 -5.1742416717200301e-01
9 4.8925439897630674e-01 1.0664717371371024e+00 -1.5557261361134094e+00
10 4.4248864855928816e-01 -3.0350413488311634e-01 -1.3898451367617182e-01
11 1.6560442813187830e+00 -1.5966304279484356e-01 -1.4963812385239397e+00
12 9.5494331320688497e-01 3.4281550160266666e-01 -1.2977588148095516e+00
13 5.3080735403713286e-01 9.0812431025473794e-01 -1.4389316642918708e+00
14 -1.8067673652119607e+00 2.5646079989138193e-01 1.5503065653205788e+00
15 -2.2860558945796523e+00 1.7347982044145904e-01 2.1125760741381931e+00
16 6.1857755737751563e-01 1.7746835837124604e+00 -2.3932611410899760e+00
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29 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
...

54
unittest/force-styles/tests/fix-timestep-efield_region.yaml
View File

@ -1,6 +1,7 @@
---
lammps_version: 17 Feb 2022
date_generated: Fri Mar 18 22:17:58 2022
lammps_version: 27 Jun 2024
tags: generated
date_generated: Sat Aug 3 05:18:10 2024
epsilon: 2e-13
skip_tests:
prerequisites: ! |
@ -11,8 +12,11 @@ post_commands: ! |
region half block 0 EDGE EDGE EDGE EDGE EDGE
fix move all nve
fix test solute efield 0.1 0.1 0.1 region half
fix_modify test virial yes
input_file: in.fourmol
natoms: 29
run_stress: ! |2-
1.1952991612400572e+00 1.9458378941195973e+00 -3.1399685374218067e-01 1.9458378941195973e+00 -3.1399685374218067e-01 -3.1399685374218067e-01
global_scalar: -2.8271402016174743
global_vector: ! |-
3 0.714877019 0.714877019 0.714877019
@ -47,33 +51,33 @@ run_pos: ! |2
28 -2.7473562684514778e+00 -4.0200819932382421e+00 1.5830052163435122e+00
29 -1.3126000191360516e+00 -3.5962518039482134e+00 2.2746342468738145e+00
run_vel: ! |2
1 8.1708759711752958e-03 1.6517639874638803e-02 4.7902879389058383e-03
2 5.5964331165928010e-03 5.3239383069183174e-03 -1.2861059284729379e-03
3 -8.2292637161143385e-03 -1.2926128087381868e-02 -4.0984161443673190e-03
1 8.1708759711752975e-03 1.6517639874638803e-02 4.7902879389058340e-03
2 5.5964331165928010e-03 5.3239383069183226e-03 -1.2861059284729340e-03
3 -8.2292637161143403e-03 -1.2926128087381868e-02 -4.0984161443673173e-03
4 -3.7697526145864203e-03 -6.5725127853647532e-03 -1.1187560499435428e-03
5 -1.1022006462580933e-02 -9.8906385073934400e-03 -2.8410749782010374e-03
5 -1.1022006462580933e-02 -9.8906385073934400e-03 -2.8410749782010383e-03
6 -3.9598958324881833e-02 4.6903198210396124e-02 3.7196915155023061e-02
7 8.4653619788661286e-04 -1.0186461918106198e-02 -5.1609252834488979e-02
7 8.4653619788661264e-04 -1.0186461918106198e-02 -5.1609252834488979e-02
8 7.8471683791752362e-03 -3.4193297369123185e-03 3.4507457170165158e-02
9 1.7075694205393060e-03 3.8777304373514634e-03 1.5162863367694195e-02
9 1.7075694205393051e-03 3.8777304373514639e-03 1.5162863367694195e-02
10 2.9215614627888371e-02 -2.9240701545949585e-02 -1.5006701597915331e-02
11 -4.7405866731533054e-03 -3.7068192956066894e-03 -2.3045121721450906e-03
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13 2.7935114371385656e-03 5.8586940588092199e-03 -7.5304481929041526e-04
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11 -4.7405866731533063e-03 -3.7068192956066894e-03 -2.3045121721450897e-03
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13 2.7935114371385635e-03 5.8586940588092181e-03 -7.5304481929041461e-04
14 3.5665654501702677e-03 -5.7512922858593447e-03 -3.9089424767000365e-03
15 -1.8139594485811841e-03 -5.8166150528014202e-03 6.3351631624150228e-03
16 1.8770941362463107e-02 -1.3183631365002509e-02 -4.5573108750104258e-02
17 -1.2963606226862703e-02 9.6937549225388098e-03 3.7247063085491160e-02
18 -8.0065796921844994e-04 -8.6270475993526386e-04 -1.4483040616159765e-03
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20 3.5930060224885880e-03 3.6938860305007859e-03 3.2322732691378846e-03
21 -1.4689220363177679e-03 -2.7352129611332704e-04 7.0581624058295520e-04
22 -7.0694199254319476e-03 -4.2577148923730610e-03 2.8079117602693740e-04
23 6.0446963117453019e-03 -1.4000131613672311e-03 2.5819754846776472e-03
24 3.1926367807141095e-04 -9.9445664297286387e-04 1.4999997144977533e-04
25 1.3789754489252400e-04 -4.4335894881614539e-03 -8.1808136766960723e-04
26 2.0485904035389413e-03 2.7813358635286672e-03 4.3245727149205113e-03
27 4.5604120798143971e-04 -1.0305522996113419e-03 2.1188058145416930e-04
28 -6.2544520867286501e-03 1.4127711163405999e-03 -1.8429821880090427e-03
29 6.4110631523949934e-04 3.1273432721623264e-03 3.7253671106301819e-03
18 -8.0065796921844994e-04 -8.6270475993526386e-04 -1.4483040616159767e-03
19 1.2452390834561398e-03 -2.5061097124141909e-03 7.2998631012995037e-03
20 3.5930060224885880e-03 3.6938860305007859e-03 3.2322732691378851e-03
21 -1.4689220363177679e-03 -2.7352129611332672e-04 7.0581624058295423e-04
22 -7.0694199254319502e-03 -4.2577148923730627e-03 2.8079117602693848e-04
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...

60
unittest/force-styles/tests/fix-timestep-efield_variable.yaml
View File

@ -1,6 +1,7 @@
---
lammps_version: 17 Feb 2022
date_generated: Fri Mar 18 22:17:58 2022
lammps_version: 27 Jun 2024
tags: generated
date_generated: Sat Aug 3 05:18:19 2024
epsilon: 2e-13
skip_tests:
prerequisites: ! |
@ -15,8 +16,11 @@ post_commands: ! |
variable zforce equal 0.1*step/10.0
fix move all nve
fix test solute efield v_xforce 0.0 v_zforce
fix_modify test virial yes
input_file: in.fourmol
natoms: 29
run_stress: ! |2-
0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
global_scalar: 0
global_vector: ! |-
3 10.275935322301738 0 -1.1102230246251565e-16
@ -51,33 +55,33 @@ run_pos: ! |2
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run_vel: ! |2
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...

77
unittest/force-styles/tests/fix-timestep-gravity.yaml Normal file
View File

@ -0,0 +1,77 @@
---
lammps_version: 17 Apr 2024
tags: generated
date_generated: Fri Jun 7 18:18:25 2024
epsilon: 2e-14
skip_tests:
prerequisites: ! |
atom full
fix gravity
pre_commands: ! ""
post_commands: ! |
fix move all nve
fix test solute gravity 1.0 chute 24.0
input_file: in.fourmol
natoms: 29
global_scalar: -186.21588194703688
run_pos: ! |2
1 -2.7011524053324809e-01 2.4912159905686591e+00 -1.6772297284757851e-01
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run_vel: ! |2
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29 6.4110630400058470e-04 3.1273432599821832e-03 3.7253671183308450e-03
...

71
unittest/force-styles/tests/fix-timestep-nph_sphere.yaml
View File

@ -1,7 +1,8 @@
---
lammps_version: 17 Feb 2022
date_generated: Fri Mar 18 22:17:59 2022
epsilon: 2e-13
lammps_version: 27 Jun 2024
tags: generated
date_generated: Sun Aug 4 23:15:54 2024
epsilon: 1e-12
skip_tests:
prerequisites: ! |
atom full
@ -16,9 +17,9 @@ post_commands: ! |
fix test solute nph/sphere aniso 1.0 1.0 100.0 ptemp ${t_target} fixedpoint 0.0 0.0 0.0 couple xy
input_file: in.dipole
natoms: 29
global_scalar: 2.6530736625996387
global_scalar: 2.6530736625996396
global_vector: ! |-
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run_pos: ! |2
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2 3.0951603206194456e-01 2.9505189917751125e+00 -8.3691694167351027e-01
@ -50,22 +51,22 @@ run_pos: ! |2
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run_vel: ! |2
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@ -79,4 +80,34 @@ run_vel: ! |2
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run_torque: ! |2
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22 -3.4861177509964607e+00 -3.5697227554916346e+01 -2.9750776757149413e+01
23 -8.2634839072258348e+00 3.3737771191416826e+01 -1.2660276418845287e+01
24 1.8703854501504455e+01 -1.5645088023891809e+01 -2.2733605897829513e+01
25 1.5612004327982518e+00 -8.2018511111335837e+00 -2.8085016931855002e+01
26 2.0140400378282479e+01 -7.8754459706884248e+00 -1.0601583601036417e+01
27 -1.0975843760114651e+01 -3.9669607217153306e+01 -5.1221146281394347e+01
28 3.8358449521425966e+00 2.0130999061460240e+00 -1.3672233012382646e+00
29 2.4433070051020643e+01 4.2903727282924805e+01 -2.2734945786369632e+01
...

59
unittest/force-styles/tests/fix-timestep-npt_sphere_aniso.yaml
View File

@ -1,6 +1,7 @@
---
lammps_version: 17 Feb 2022
date_generated: Fri Mar 18 22:17:59 2022
lammps_version: 27 Jun 2024
tags: generated
date_generated: Sun Aug 4 23:03:14 2024
epsilon: 4e-13
skip_tests:
prerequisites: ! |
@ -16,9 +17,9 @@ post_commands: ! |
fix test solute npt/sphere temp 50.0 ${t_target} 1.0 aniso 1.0 1.0 100.0 drag 0.01 flip no
input_file: in.dipole
natoms: 29
global_scalar: 12.096663886115623
global_scalar: 12.09666388611562
global_vector: ! |-
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run_pos: ! |2
1 -2.7397105633323537e-01 2.4781785743666527e+00 -1.7980596873158383e-01
2 3.1208634768681343e-01 2.9563521874575622e+00 -8.4152963592209495e-01
@ -50,22 +51,22 @@ run_pos: ! |2
28 -2.7298172127749782e+00 -4.0269250728459882e+00 1.5452330932758489e+00
29 -1.3036629303295193e+00 -3.6048159970063285e+00 2.2185254278264974e+00
run_vel: ! |2
1 6.6645514337822221e-04 6.0192577730141302e-04 -3.7299030694254800e-04
2 4.4186462683745379e-03 -4.6840896920226343e-03 6.9463033422740798e-03
3 -8.2788283512656355e-04 1.6664323303816283e-03 -3.6067014934863556e-04
4 -2.3360131422093099e-03 -2.4652356574843341e-04 -6.7612095269435129e-03
1 6.6645514337822231e-04 6.0192577730141302e-04 -3.7299030694254806e-04
2 4.4186462683745396e-03 -4.6840896920226326e-03 6.9463033422740798e-03
3 -8.2788283512656355e-04 1.6664323303816279e-03 -3.6067014934863551e-04
4 -2.3360131422093108e-03 -2.4652356574843422e-04 -6.7612095269435129e-03
5 -9.9515654282019347e-03 -1.0186535017680895e-02 7.0490084717633053e-03
6 -6.3804753331014364e-05 1.1107780038266837e-03 4.6244242981496387e-04
7 -3.0142488152500515e-05 -5.6684692709220636e-04 -5.9335396255129249e-04
8 2.1070083677950848e-04 -5.2394803973737354e-04 6.1467530744658834e-04
9 3.6195183545487952e-03 -8.3369682502568449e-03 -1.6601527132808564e-02
10 3.2079212235368532e-04 6.8314953697639464e-04 -1.4658709900665799e-04
9 3.6195183545487952e-03 -8.3369682502568432e-03 -1.6601527132808564e-02
10 3.2079212235368521e-04 6.8314953697639464e-04 -1.4658709900665799e-04
11 -3.7785845503840996e-03 -6.5404736905947487e-03 -6.2889329470937165e-03
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13 -1.3242589815117630e-03 1.6385138464187414e-03 -5.7720431286344674e-04
12 9.6291409057966740e-04 -6.5439203151497092e-04 -1.4918221706275551e-03
13 -1.3242589815117625e-03 1.6385138464187401e-03 -5.7720431286344717e-04
14 3.1480939042203030e-03 -7.0000358651570562e-03 2.4177974139595096e-03
15 -3.3454335023896131e-03 4.4058024755002799e-04 1.4883635219226489e-02
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15 -3.3454335023896152e-03 4.4058024755002799e-04 1.4883635219226489e-02
16 -1.7846013433072089e-04 -2.8806672944350730e-04 1.5882710120078808e-03
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18 -6.0936815808025862e-04 -9.3774557532468582e-04 -3.3558072507805731e-04
19 -6.9919768291957119e-04 -3.6060777270430031e-03 4.2833405289822791e-03
@ -79,4 +80,34 @@ run_vel: ! |2
27 -2.6510179146429716e-04 3.6306203629019116e-04 -5.6235585400647747e-04
28 -2.3068708109787484e-04 -8.5663070212203200e-04 2.1302563179109169e-03
29 -2.5054744388303732e-03 -1.6773997805290820e-04 2.8436699761004796e-03
run_torque: ! |2
1 -6.0660818391266602e+00 1.9626142015743959e+01 3.7810315455845227e+01
2 3.1086627430245031e+01 3.1559922086010953e+01 3.3385905729180720e+01
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6 -5.8025493341725245e+01 1.0466802807207529e+01 1.0911933765209140e+01
7 1.6893959738182637e+01 2.2082773261488860e+01 1.3985144361215289e+01
8 -4.5187945100859821e+01 3.0772942031362557e+01 7.6461850322358078e+00
9 -1.5180502321667255e+01 -3.4199898773076569e+01 4.8547447534871750e+01
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11 1.0442950702528758e+01 7.6816289767997219e+01 7.1166317558599355e+00
12 -3.5964317585734498e+00 -8.1220469491431153e+00 2.0923830245103037e+01
13 -2.5929181494647704e+01 -3.2833031788579881e+00 5.7968524934518165e+01
14 -2.0295740978463765e+01 2.5641485002706430e+00 5.0370803328630622e+01
15 -3.7219665122688724e+01 2.2710632544675340e+00 3.3747728711895171e+01
16 8.9845518011810181e+00 2.2562606948955214e+01 1.3731908367575469e+00
17 -1.3257834489616751e+01 1.1571932592993791e+01 -2.7222135722054990e+00
18 3.6797531368782984e+01 -4.8449756711271370e+01 4.6735301744348575e+01
19 -3.6539921027013356e+00 -1.4434974695842002e+00 2.1465476017408964e+01
20 5.8197218381159274e+01 -2.4226041453460791e+01 -7.2276449578839550e+00
21 -1.5833118978634616e+01 -1.5011099827401669e+01 2.0299638507345083e+01
22 -3.5901038361540287e+00 -3.6231138768557685e+01 -3.0226233062003047e+01
23 -8.4961498180872912e+00 3.4214654432737127e+01 -1.2845241682264085e+01
24 1.8945253142131943e+01 -1.5910276330193202e+01 -2.3294771297456020e+01
25 1.4926980431453991e+00 -8.2573776498377303e+00 -2.8232701560097244e+01
26 2.0312538690670358e+01 -7.8590237308018986e+00 -1.0821678612971260e+01
27 -1.1320545333645292e+01 -3.9980842064526570e+01 -5.1295313234694916e+01
28 3.6290258946306180e+00 1.8294018697218410e+00 -1.2938753473310651e+00
29 2.4092346285942053e+01 4.3370903825013755e+01 -2.2770854107671028e+01
...

65
unittest/force-styles/tests/fix-timestep-npt_sphere_iso.yaml
View File

@ -1,7 +1,8 @@
---
lammps_version: 17 Feb 2022
date_generated: Fri Mar 18 22:17:59 2022
epsilon: 2e-13
lammps_version: 27 Jun 2024
tags: generated
date_generated: Sun Aug 4 23:03:30 2024
epsilon: 1e-12
skip_tests:
prerequisites: ! |
atom full
@ -16,9 +17,9 @@ post_commands: ! |
fix test solute npt/sphere temp 50.0 ${t_target} 1.0 iso 1.0 1.0 100.0 dilate solute
input_file: in.dipole
natoms: 29
global_scalar: 9.042301471806708
global_scalar: 9.04230147180671
global_vector: ! |-
28 0.1863641554205169 1.420148091453985 -1.1292034459301246 0.09086316406911916 1.9990627120668834 0.47615124832482786 -0.006387790127403963 -0.00558070983166458 0.0010748001531976797 -0.00023261555228169703 -0.00023292456865841747 0.0020841825580977056 -0.00023513173250148996 -0.00023642170879896256 6.332884080784521 0.28221278023295715 -0.2243960653415431 0.14027648316892322 0.39706891031681196 0.02252697627211294 -0.000934258230287154 2.0887944455121046 0.00021358500655954555 -4.6225518401838857e-05 -4.628692634326172e-05 0.0032370232941587745 4.1199960358459955e-05 4.165326165323854e-05
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run_pos: ! |2
1 -2.6730556919536941e-01 2.4568877649772691e+00 -1.7525449543283766e-01
2 3.1651774679036304e-01 2.9312403511996870e+00 -8.4441875599840355e-01
@ -50,21 +51,21 @@ run_pos: ! |2
28 -2.7406520384725965e+00 -4.0207251278130975e+00 1.5828689861678511e+00
29 -1.3108232656499081e+00 -3.5992986322410760e+00 2.2680459788743503e+00
run_vel: ! |2
1 6.7245251088027887e-04 6.1138248355858786e-04 -3.7339702570044338e-04
2 4.4052559672891761e-03 -4.6696302057353299e-03 6.9799826311339004e-03
3 -8.4229974223012048e-04 1.6692222625580460e-03 -3.4811445486190135e-04
4 -2.3115850080186896e-03 -2.1921753106846976e-04 -6.6129202326324875e-03
1 6.7245251088027887e-04 6.1138248355858764e-04 -3.7339702570044338e-04
2 4.4052559672891761e-03 -4.6696302057353291e-03 6.9799826311339021e-03
3 -8.4229974223012048e-04 1.6692222625580464e-03 -3.4811445486190130e-04
4 -2.3115850080186900e-03 -2.1921753106847122e-04 -6.6129202326324875e-03
5 -9.9270913083732166e-03 -1.0162835960427124e-02 6.6835450876805242e-03
6 -6.3349132255598176e-05 1.1213920888471765e-03 4.3957112467583707e-04
7 -3.0550264536359436e-05 -5.7212395421602175e-04 -5.7852611868756802e-04
8 2.1230260290084160e-04 -5.2946150247993511e-04 6.1002092957609434e-04
9 3.5835237205891044e-03 -8.2976423766382163e-03 -1.6569654205811610e-02
10 3.2215400971380464e-04 6.7777051599916360e-04 -1.4690970683667591e-04
11 -3.8262569070299369e-03 -6.4899437483942309e-03 -6.0625717608142051e-03
12 9.6903366708958486e-04 -6.5830810892723922e-04 -1.4851103246954738e-03
13 -1.3051803182304389e-03 1.5782109043276430e-03 -5.7359190198993059e-04
14 3.1570944675627741e-03 -6.9925437658747589e-03 2.5670995049832746e-03
15 -3.3107454411357724e-03 5.6059336622465679e-04 1.4845717250576757e-02
8 2.1230260290084160e-04 -5.2946150247993511e-04 6.1002092957609445e-04
9 3.5835237205891039e-03 -8.2976423766382163e-03 -1.6569654205811610e-02
10 3.2215400971380464e-04 6.7777051599916360e-04 -1.4690970683667594e-04
11 -3.8262569070299374e-03 -6.4899437483942292e-03 -6.0625717608142043e-03
12 9.6903366708958486e-04 -6.5830810892723943e-04 -1.4851103246954738e-03
13 -1.3051803182304387e-03 1.5782109043276438e-03 -5.7359190198992950e-04
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15 -3.3107454411357724e-03 5.6059336622465647e-04 1.4845717250576757e-02
16 -1.8030723242303502e-04 -2.9205235801445917e-04 1.5828900167446096e-03
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18 -6.0936815808025862e-04 -9.3774557532468582e-04 -3.3558072507805731e-04
@ -79,4 +80,34 @@ run_vel: ! |2
27 -2.6510179146429716e-04 3.6306203629019116e-04 -5.6235585400647747e-04
28 -2.3068708109787484e-04 -8.5663070212203200e-04 2.1302563179109169e-03
29 -2.5054744388303732e-03 -1.6773997805290820e-04 2.8436699761004796e-03
run_torque: ! |2
1 -6.0554110246137771e+00 1.9847575898948492e+01 3.8198295167231464e+01
2 3.0670154989358359e+01 3.0869771736844150e+01 3.2281895844842595e+01
3 2.2350393637174943e+01 9.7433278995078823e+00 1.0139982748947251e+01
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8 -4.4090277831995607e+01 3.0850568334747003e+01 7.8191692458467950e+00
9 -1.5149678159864287e+01 -3.2837983461253856e+01 4.8126635558511659e+01
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15 -3.8842882009303608e+01 1.9933563583102023e+00 3.4778718592720743e+01
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22 -3.2616079590092801e+00 -3.5263943061632084e+01 -2.9282541013692690e+01
23 -8.1241593398597960e+00 3.3321305667998743e+01 -1.2502058995490415e+01
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27 -1.0257782620802805e+01 -3.9202065451935738e+01 -5.1363492997585205e+01
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29 2.4630674102439567e+01 4.2565916677290893e+01 -2.2691969241133958e+01
...

125
unittest/force-styles/tests/fix-timestep-npt_sphere_tri.yaml
View File

@ -1,6 +1,7 @@
---
lammps_version: 17 Feb 2022
date_generated: Fri Mar 18 22:17:59 2022
lammps_version: 27 Jun 2024
tags: generated
date_generated: Sun Aug 4 23:05:01 2024
epsilon: 1e-12
skip_tests:
prerequisites: ! |
@ -17,57 +18,57 @@ post_commands: ! |
fix test solute npt/sphere temp 50.0 ${t_target} 1.0 tri 1.0 1.0 100.0 nreset 2
input_file: in.dipole
natoms: 29
global_scalar: 12.427074202242965
global_scalar: 12.427074202242943
global_vector: ! |-
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...

55
unittest/force-styles/tests/fix-timestep-nve_sphere.yaml
View File

@ -1,6 +1,7 @@
---
lammps_version: 17 Feb 2022
date_generated: Fri Mar 18 22:17:59 2022
lammps_version: 27 Jun 2024
tags: generated
date_generated: Sun Aug 4 23:05:44 2024
epsilon: 5e-14
skip_tests:
prerequisites: ! |
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...

61
unittest/force-styles/tests/fix-timestep-nve_sphere_dipole.yaml
View File

@ -1,6 +1,7 @@
---
lammps_version: 17 Feb 2022
date_generated: Fri Mar 18 22:17:59 2022
lammps_version: 27 Jun 2024
tags: generated
date_generated: Sun Aug 4 23:06:12 2024
epsilon: 5e-14
skip_tests:
prerequisites: ! |
@ -47,22 +48,22 @@ run_pos: ! |2
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@ -76,4 +77,34 @@ run_vel: ! |2
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run_torque: ! |2
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...

65
unittest/force-styles/tests/fix-timestep-nve_sphere_dipole_dlm.yaml
View File

@ -1,7 +1,8 @@
---
lammps_version: 17 Feb 2022
date_generated: Fri Mar 18 22:17:59 2022
epsilon: 5e-14
lammps_version: 27 Jun 2024
tags: generated
date_generated: Sun Aug 4 23:06:24 2024
epsilon: 1e-09
skip_tests:
prerequisites: ! |
atom full
@ -47,22 +48,22 @@ run_pos: ! |2
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29 -1.3108232656499081e+00 -3.5992986322410760e+00 2.2680459788743503e+00
run_vel: ! |2
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@ -76,4 +77,34 @@ run_vel: ! |2
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run_torque: ! |2
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...

63
unittest/force-styles/tests/fix-timestep-nvt_sphere.yaml
View File

@ -1,6 +1,7 @@
---
lammps_version: 17 Feb 2022
date_generated: Fri Mar 18 22:17:59 2022
lammps_version: 27 Jun 2024
tags: generated
date_generated: Sun Aug 4 23:11:49 2024
epsilon: 5e-14
skip_tests:
prerequisites: ! |
@ -16,9 +17,9 @@ post_commands: ! |
fix test solute nvt/sphere temp 50.0 ${t_target} 1.0 mtk no tchain 1
input_file: in.dipole
natoms: 29
global_scalar: 9.924697652139484
global_scalar: 9.924697652139486
global_vector: ! |-
4 0.437308072017019 0.3665139279582143 8.603313153695396 1.3213844984440877
4 0.43730807201701904 0.36651392795821436 8.603313153695398 1.3213844984440881
run_pos: ! |2
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2 3.0850115944710327e-01 2.9513142622511719e+00 -8.4681556480583575e-01
@ -50,22 +51,22 @@ run_pos: ! |2
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run_vel: ! |2
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@ -79,4 +80,34 @@ run_vel: ! |2
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29 -2.5054744388303732e-03 -1.6773997805290820e-04 2.8436699761004796e-03
run_torque: ! |2
1 -6.1647479505817486e+00 1.9357854481281628e+01 3.7382095469801669e+01
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...

133
unittest/force-styles/tests/fix-timestep-wall_lj93_const.yaml
View File

@ -1,82 +1,83 @@
---
lammps_version: 17 Feb 2022
date_generated: Fri Mar 18 22:18:01 2022
lammps_version: 27 Jun 2024
tags: generated
date_generated: Fri Aug 2 23:56:34 2024
epsilon: 2e-14
skip_tests:
prerequisites: ! |
atom full
fix wall/lj93
pre_commands: ! |
boundary p f p
boundary f f f
post_commands: ! |
fix move all nve
fix test solute wall/lj93 ylo EDGE 100.0 2.0 5.0 yhi EDGE 100.0 2.0 5.0
fix test solute wall/lj93 xlo EDGE 10 1 9 xhi EDGE 20 2 8 ylo EDGE 30 3 7 yhi EDGE 40 4 6 zlo EDGE 50 9 1 zhi EDGE 60 8 2
fix_modify test virial yes
input_file: in.fourmol
natoms: 29
run_stress: ! |2-
0.0000000000000000e+00 -5.0602303343219951e+01 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
global_scalar: -4.108987997282236
run_stress: ! |-
-2.0397146716028331e+01 -2.2856621254611628e+02 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
global_scalar: -40.30685365068726
global_vector: ! |-
2 0 -11.164431050504302
6 0.29980999393772645 -3.0501185308112175 10.543906177602482 -35.13125907303744 0 0
run_pos: ! |2
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run_vel: ! |2
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...

78
unittest/force-styles/tests/fix-timestep-wall_reflect.yaml Normal file
View File

@ -0,0 +1,78 @@
---
lammps_version: 17 Apr 2024
tags: generated
date_generated: Fri Jun 7 18:23:44 2024
epsilon: 4e-14
skip_tests:
prerequisites: ! |
atom full
fix nve
fix wall/reflect
pre_commands: ! |
boundary f f f
post_commands: ! |
fix move all nve
fix test solute wall/reflect xlo EDGE xhi EDGE ylo EDGE yhi EDGE zlo EDGE zhi EDGE units box
input_file: in.fourmol
natoms: 29
run_pos: ! |2
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run_vel: ! |2
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9 1.5644176117320932e-03 3.7365546102722212e-03 1.5047408822037651e-02
10 2.9201446820573192e-02 -2.9249578745486147e-02 -1.5018077424322544e-02
11 -4.7835961513517542e-03 -3.7481385134185202e-03 -2.3464104142290089e-03
12 2.2696451841920694e-03 -3.4774154398129690e-04 -3.0640770327796979e-03
13 2.7531740451953164e-03 5.8171061612840493e-03 -7.9467454022160377e-04
14 3.5246182371994183e-03 -5.7939995585585503e-03 -3.9478431172751344e-03
15 -1.8547943640122972e-03 -5.8554729942777778e-03 6.2938485140538692e-03
16 1.8681499973445252e-02 -1.3262466204585332e-02 -4.5638651457003250e-02
17 -1.2896269981100378e-02 9.7527665265956451e-03 3.7296535360836762e-02
18 -8.0065795274987550e-04 -8.6270473974390605e-04 -1.4483040536385806e-03
19 1.2452390067376805e-03 -2.5061097800836356e-03 7.2998639311871892e-03
20 3.5930058460518109e-03 3.6938852051849871e-03 3.2322738480194770e-03
21 -1.4689219756961604e-03 -2.7352107824530231e-04 7.0581625180892046e-04
22 -7.0694199165145140e-03 -4.2577148692717554e-03 2.8079117911323815e-04
23 6.0446963236685256e-03 -1.4000131545098772e-03 2.5819754799379755e-03
24 3.1926368451268056e-04 -9.9445664487428712e-04 1.4999960207062358e-04
25 1.3789752933078488e-04 -4.4335894831520773e-03 -8.1808138106080109e-04
26 2.0485904023410002e-03 2.7813358660936120e-03 4.3245726853349290e-03
27 4.5604120293369819e-04 -1.0305523026921102e-03 2.1188058381358391e-04
28 -6.2544520861855151e-03 1.4127711176146864e-03 -1.8429821884794260e-03
29 6.4110631534402261e-04 3.1273432719593807e-03 3.7253671105656745e-03
...

4
unittest/utils/test_fmtlib.cpp
View File

@ -126,11 +126,11 @@ TEST(FmtLib, insert_neg_double)
TEST(FmtLib, int_for_double)
{
const double val = -1.5;
ASSERT_THROW(fmt::format("word {:d}", val), std::exception);
ASSERT_THROW(auto text = fmt::format("word {:d}", val), std::exception);
}
TEST(FmtLib, double_for_int)
{
const int val = 15;
ASSERT_THROW(fmt::format("word {:g}", val), std::exception);
ASSERT_THROW(auto text = fmt::format("word {:g}", val), std::exception);
}