From 7c90c9f2e9a4296d4a51fa6447420214ea902de3 Mon Sep 17 00:00:00 2001
From: "Kurt A. O'Hearn" <ohearnku@msu.edu>
Date: Thu, 18 Feb 2021 17:20:39 -0500
Subject: [PATCH] Test: fix Python wrapper for QM/MM (interfaces out-of-date).
Fix Fortran tester bugs. Add test artifacts.
---
PG-PuReMD/src/cuda/cuda_bonds.cu | 61 +-
PG-PuReMD/src/cuda/cuda_forces.cu | 136 ++-
PG-PuReMD/src/cuda/cuda_multi_body.cu | 80 +-
PG-PuReMD/src/cuda/cuda_torsion_angles.cu | 216 +++--
PG-PuReMD/src/cuda/cuda_valence_angles.cu | 498 +++++------
PG-PuReMD/src/cuda/cuda_valence_angles.h | 9 +-
PG-PuReMD/src/reax_types.h | 4 +-
test/library/qmmm_amber/forces_charges.txt | 777 ++++++++++++++++++
.../qmmm_amber/fortran_stub/driver.F03 | 26 +-
.../fortran_stub/forces_charges.txt | 776 +++++++++++++++++
.../qmmm_amber/fortran_stub/reaxff_puremd.F03 | 2 +-
.../qmmm_amber/fortran_stub/run_sim.bash | 3 +-
test/library/qmmm_amber/tester_AVE.py | 13 +-
13 files changed, 2067 insertions(+), 534 deletions(-)
create mode 100644 test/library/qmmm_amber/forces_charges.txt
create mode 100644 test/library/qmmm_amber/fortran_stub/forces_charges.txt
diff --git a/PG-PuReMD/src/cuda/cuda_bonds.cu b/PG-PuReMD/src/cuda/cuda_bonds.cu
index 9cd4e0a4..5a705b17 100644
--- a/PG-PuReMD/src/cuda/cuda_bonds.cu
+++ b/PG-PuReMD/src/cuda/cuda_bonds.cu
@@ -30,14 +30,17 @@
CUDA_GLOBAL void Cuda_Bonds( reax_atom *my_atoms, global_parameters gp,
single_body_parameters *sbp, two_body_parameters *tbp,
storage p_workspace, reax_list p_bond_list, int n, int num_atom_types,
- real *e_bond )
+ real *e_bond_g )
{
int i, j, pj;
int start_i, end_i;
int type_i, type_j;
- real ebond, pow_BOs_be2, exp_be12, CEbo;
+ real pow_BOs_be2, exp_be12, CEbo;
+#if defined(CUDA_ACCUM_ENERGY_ATOMIC)
+ real e_bond_l;
+#endif
real gp3, gp4, gp7, gp10, gp37;
- real exphu, exphua1, exphub1, exphuov, hulpov, estriph;
+ real exphu, exphua1, exphub1, exphuov, hulpov;
real decobdbo, decobdboua, decobdboub;
single_body_parameters *sbp_i, *sbp_j;
two_body_parameters *twbp;
@@ -59,6 +62,9 @@ CUDA_GLOBAL void Cuda_Bonds( reax_atom *my_atoms, global_parameters gp,
gp7 = gp.l[7];
gp10 = gp.l[10];
gp37 = (int) gp.l[37];
+#if defined(CUDA_ACCUM_ENERGY_ATOMIC)
+ e_bond_l = 0.0;
+#endif
start_i = Start_Index( i, bond_list );
end_i = End_Index( i, bond_list );
@@ -82,32 +88,21 @@ CUDA_GLOBAL void Cuda_Bonds( reax_atom *my_atoms, global_parameters gp,
* (1.0 - twbp->p_be1 * twbp->p_be2 * pow_BOs_be2);
/* calculate bond energy */
- ebond = -twbp->De_s * bo_ij->BO_s * exp_be12
+#if !defined(CUDA_ACCUM_ENERGY_ATOMIC)
+ e_bond_g[i] += -twbp->De_s * bo_ij->BO_s * exp_be12
+ - twbp->De_p * bo_ij->BO_pi
+ - twbp->De_pp * bo_ij->BO_pi2;
+#else
+ e_bond_l += -twbp->De_s * bo_ij->BO_s * exp_be12
- twbp->De_p * bo_ij->BO_pi
- twbp->De_pp * bo_ij->BO_pi2;
- e_bond[i] += ebond;
+#endif
/* calculate derivatives of bond orders */
bo_ij->Cdbo += CEbo;
bo_ij->Cdbopi -= CEbo + twbp->De_p;
bo_ij->Cdbopi2 -= CEbo + twbp->De_pp;
-#if defined(TEST_ENERGY)
- //fprintf( out_control->ebond, "%6d%6d%24.15e%24.15e%24.15e\n",
- fprintf( out_control->ebond, "%6d%6d%12.4f%12.4f%12.4f\n",
- system->my_atoms[i].orig_id,
- system->my_atoms[j].orig_id,
- bo_ij->BO, ebond, data->my_en.e_bond );
-#endif
-
-#if defined(TEST_FORCES)
- Add_dBO( system, lists, i, pj, CEbo, workspace->f_be );
- Add_dBOpinpi2( system, lists, i, pj,
- -(CEbo + twbp->De_p),
- -(CEbo + twbp->De_pp),
- workspace->f_be, workspace->f_be );
-#endif
-
/* Stabilisation terminal triple bond */
if ( bo_ij->BO >= 1.00 )
{
@@ -127,8 +122,11 @@ CUDA_GLOBAL void Cuda_Bonds( reax_atom *my_atoms, global_parameters gp,
exphuov = EXP(gp4 * (workspace->Delta[i] + workspace->Delta[j]));
hulpov = 1.0 / (1.0 + 25.0 * exphuov);
- estriph = gp10 * exphu * hulpov * (exphua1 + exphub1);
- e_bond[i] += estriph;
+#if !defined(CUDA_ACCUM_ENERGY_ATOMIC)
+ e_bond_g[i] += gp10 * exphu * hulpov * (exphua1 + exphub1);
+#else
+ e_bond_l += gp10 * exphu * hulpov * (exphua1 + exphub1);
+#endif
decobdbo = gp10 * exphu * hulpov * (exphua1 + exphub1)
* ( gp3 - 2.0 * gp7 * (bo_ij->BO - 2.5) );
@@ -140,21 +138,12 @@ CUDA_GLOBAL void Cuda_Bonds( reax_atom *my_atoms, global_parameters gp,
bo_ij->Cdbo += decobdbo;
workspace->CdDelta[i] += decobdboua;
workspace->CdDelta[j] += decobdboub;
-
-#if defined(TEST_ENERGY)
- //fprintf( out_control->ebond,
- // "%6d%6d%24.15e%24.15e%24.15e%24.15e\n",
- // system->my_atoms[i].orig_id, system->my_atoms[j].orig_id,
- // estriph, decobdbo, decobdboua, decobdboub );
-#endif
-
-#if defined(TEST_FORCES)
- Add_dBO( system, lists, i, pj, decobdbo, workspace->f_be );
- Add_dDelta( system, lists, i, decobdboua, workspace->f_be );
- Add_dDelta( system, lists, j, decobdboub, workspace->f_be );
-#endif
}
}
}
}
+
+#if defined(CUDA_ACCUM_ENERGY_ATOMIC)
+ atomicAdd( (double *) e_bond_g, (double) e_bond_l );
+#endif
}
diff --git a/PG-PuReMD/src/cuda/cuda_forces.cu b/PG-PuReMD/src/cuda/cuda_forces.cu
index 6c658975..f0310b5f 100644
--- a/PG-PuReMD/src/cuda/cuda_forces.cu
+++ b/PG-PuReMD/src/cuda/cuda_forces.cu
@@ -223,7 +223,6 @@ CUDA_GLOBAL void k_init_distance( reax_atom *my_atoms, reax_list far_nbr_list, i
{
int i, j, pj, start_i, end_i;
rvec x_i;
- reax_atom *atom_j;
i = blockIdx.x * blockDim.x + threadIdx.x;
@@ -240,19 +239,18 @@ CUDA_GLOBAL void k_init_distance( reax_atom *my_atoms, reax_list far_nbr_list, i
for ( pj = start_i; pj < end_i; ++pj )
{
j = far_nbr_list.far_nbr_list.nbr[pj];
- atom_j = &my_atoms[j];
if ( i < j )
{
- far_nbr_list.far_nbr_list.dvec[pj][0] = atom_j->x[0] - x_i[0];
- far_nbr_list.far_nbr_list.dvec[pj][1] = atom_j->x[1] - x_i[1];
- far_nbr_list.far_nbr_list.dvec[pj][2] = atom_j->x[2] - x_i[2];
+ far_nbr_list.far_nbr_list.dvec[pj][0] = my_atoms[j].x[0] - x_i[0];
+ far_nbr_list.far_nbr_list.dvec[pj][1] = my_atoms[j].x[1] - x_i[1];
+ far_nbr_list.far_nbr_list.dvec[pj][2] = my_atoms[j].x[2] - x_i[2];
}
else
{
- far_nbr_list.far_nbr_list.dvec[pj][0] = x_i[0] - atom_j->x[0];
- far_nbr_list.far_nbr_list.dvec[pj][1] = x_i[1] - atom_j->x[1];
- far_nbr_list.far_nbr_list.dvec[pj][2] = x_i[2] - atom_j->x[2];
+ far_nbr_list.far_nbr_list.dvec[pj][0] = x_i[0] - my_atoms[j].x[0];
+ far_nbr_list.far_nbr_list.dvec[pj][1] = x_i[1] - my_atoms[j].x[1];
+ far_nbr_list.far_nbr_list.dvec[pj][2] = x_i[2] - my_atoms[j].x[2];
}
far_nbr_list.far_nbr_list.d[pj] = rvec_Norm( far_nbr_list.far_nbr_list.dvec[pj] );
}
@@ -263,7 +261,7 @@ CUDA_GLOBAL void k_init_distance( reax_atom *my_atoms, reax_list far_nbr_list, i
* in the far neighbors list if it's a NOT re-neighboring step */
CUDA_GLOBAL void k_init_distance_opt( reax_atom *my_atoms, reax_list far_nbr_list, int N )
{
- int j, pj, start_i, end_i, thread_id, warp_id, lane_id;
+ int j, pj, start_i, end_i, thread_id, warp_id, lane_id, itr;
__shared__ rvec x_i;
thread_id = blockIdx.x * blockDim.x + threadIdx.x;
@@ -284,7 +282,7 @@ CUDA_GLOBAL void k_init_distance_opt( reax_atom *my_atoms, reax_list far_nbr_lis
__syncthreads( );
/* update distance and displacement vector between atoms i and j (i-j) */
- for ( pj = start_i + lane_id; pj < end_i; pj += 32 )
+ for ( itr = 0, pj = start_i + lane_id; itr < (end_i - start_i + 0x0000001F) >> 5; ++itr )
{
j = far_nbr_list.far_nbr_list.nbr[pj];
@@ -301,6 +299,8 @@ CUDA_GLOBAL void k_init_distance_opt( reax_atom *my_atoms, reax_list far_nbr_lis
far_nbr_list.far_nbr_list.dvec[pj][2] = x_i[2] - my_atoms[j].x[2];
}
far_nbr_list.far_nbr_list.d[pj] = rvec_Norm( far_nbr_list.far_nbr_list.dvec[pj] );
+
+ pj += warpSize;
}
}
@@ -1125,7 +1125,6 @@ CUDA_GLOBAL void k_update_sym_hbond_indices_opt( reax_atom *my_atoms,
thread_id = blockIdx.x * blockDim.x + threadIdx.x;
warp_id = thread_id >> 5;
- lane_id = thread_id & 0x0000001F;
if ( warp_id > N )
{
@@ -1133,6 +1132,7 @@ CUDA_GLOBAL void k_update_sym_hbond_indices_opt( reax_atom *my_atoms,
}
i = warp_id;
+ lane_id = thread_id & 0x0000001F;
start = Start_Index( my_atoms[i].Hindex, &hbond_list );
end = End_Index( my_atoms[i].Hindex, &hbond_list );
j = start + lane_id;
@@ -1564,14 +1564,13 @@ int Cuda_Init_Forces( reax_system *system, control_params *control,
if ( renbr == FALSE && dist_done == FALSE )
{
+ blocks = system->N * 32 / DEF_BLOCK_SIZE
+ + (system->N * 32 % DEF_BLOCK_SIZE == 0 ? 0 : 1);
-// blocks = system->N * 32 / DEF_BLOCK_SIZE
-// + (system->N * 32 % DEF_BLOCK_SIZE == 0 ? 0 : 1);
-
- k_init_distance <<< control->blocks_n, control->block_size_n >>>
- ( system->d_my_atoms, *(lists[FAR_NBRS]), system->N );
-// k_init_distance_opt <<< blocks, DEF_BLOCK_SIZE >>>
+// k_init_distance <<< control->blocks_n, control->block_size_n >>>
// ( system->d_my_atoms, *(lists[FAR_NBRS]), system->N );
+ k_init_distance_opt <<< blocks, DEF_BLOCK_SIZE >>>
+ ( system->d_my_atoms, *(lists[FAR_NBRS]), system->N );
cudaCheckError( );
dist_done = TRUE;
@@ -1769,10 +1768,8 @@ int Cuda_Compute_Bonded_Forces( reax_system *system, control_params *control,
static int compute_bonded_part1 = FALSE;
real *spad;
rvec *rvec_spad;
-#if defined(DEBUG_FOCUS)
- real t_start, t_elapsed;
-#endif
+#if !defined(CUDA_ACCUM_ENERGY_ATOMIC)
cuda_check_malloc( &workspace->scratch, &workspace->scratch_size,
MAX( sizeof(real) * system->n,
MAX( sizeof(real) * 3 * system->n,
@@ -1781,6 +1778,7 @@ int Cuda_Compute_Bonded_Forces( reax_system *system, control_params *control,
(sizeof(real) + sizeof(rvec)) * system->n + sizeof(rvec) * control->blocks )))),
"Cuda_Compute_Bonded_Forces::workspace->scratch" );
spad = (real *) workspace->scratch;
+#endif
update_energy = (out_control->energy_update_freq > 0
&& data->step % out_control->energy_update_freq == 0) ? TRUE : FALSE;
ret = SUCCESS;
@@ -1810,31 +1808,59 @@ int Cuda_Compute_Bonded_Forces( reax_system *system, control_params *control,
cudaCheckError( );
/* 2. Bond Energy Interactions */
+#if !defined(CUDA_ACCUM_ENERGY_ATOMIC)
cuda_memset( spad, 0, sizeof(real) * system->n,
"Compute_Bonded_Forces::spad" );
+#else
+ cuda_memset( &((simulation_data *)data->d_simulation_data)->my_en.e_bond,
+ 0, sizeof(real), "Cuda_Compute_Bonded_Forces::e_bond" );
+#endif
Cuda_Bonds <<< control->blocks, control->block_size, sizeof(real) * control->block_size >>>
( system->d_my_atoms, system->reax_param.d_gp, system->reax_param.d_sbp, system->reax_param.d_tbp,
*(workspace->d_workspace), *(lists[BONDS]),
- system->n, system->reax_param.num_atom_types, spad );
+ system->n, system->reax_param.num_atom_types,
+#if !defined(CUDA_ACCUM_ENERGY_ATOMIC)
+ spad
+#else
+ &((simulation_data *)data->d_simulation_data)->my_en.e_bond
+#endif
+ );
cudaCheckError( );
- /* reduction for E_BE */
+#if !defined(CUDA_ACCUM_ENERGY_ATOMIC)
if ( update_energy == TRUE )
{
Cuda_Reduction_Sum( spad, &((simulation_data *)data->d_simulation_data)->my_en.e_bond,
system->n );
}
+#endif
/* 3. Atom Energy Interactions */
+#if !defined(CUDA_ACCUM_ENERGY_ATOMIC)
cuda_memset( spad, 0, sizeof(real) * 3 * system->n,
"Compute_Bonded_Forces::spad" );
+#else
+ cuda_memset( &((simulation_data *)data->d_simulation_data)->my_en.e_lp,
+ 0, sizeof(real), "Cuda_Compute_Bonded_Forces::e_lp" );
+ cuda_memset( &((simulation_data *)data->d_simulation_data)->my_en.e_ov,
+ 0, sizeof(real), "Cuda_Compute_Bonded_Forces::e_ov" );
+ cuda_memset( &((simulation_data *)data->d_simulation_data)->my_en.e_un,
+ 0, sizeof(real), "Cuda_Compute_Bonded_Forces::e_un" );
+#endif
Cuda_Atom_Energy_Part1 <<< control->blocks, control->block_size >>>
( system->d_my_atoms, system->reax_param.d_gp,
system->reax_param.d_sbp, system->reax_param.d_tbp, *(workspace->d_workspace),
*(lists[BONDS]), system->n, system->reax_param.num_atom_types,
- spad, &spad[system->n], &spad[2 * system->n] );
+#if !defined(CUDA_ACCUM_ENERGY_ATOMIC)
+ spad, &spad[system->n], &spad[2 * system->n]
+#else
+ &((simulation_data *)data->d_simulation_data)->my_en.e_lp,
+ &((simulation_data *)data->d_simulation_data)->my_en.e_ov,
+ &((simulation_data *)data->d_simulation_data)->my_en.e_un
+#endif
+ );
cudaCheckError( );
#if !defined(CUDA_ACCUM_FORCE_ATOMIC)
@@ -1843,22 +1869,21 @@ int Cuda_Compute_Bonded_Forces( reax_system *system, control_params *control,
cudaCheckError( );
#endif
+#if !defined(CUDA_ACCUM_ENERGY_ATOMIC)
if ( update_energy == TRUE )
{
- /* reduction for E_Lp */
Cuda_Reduction_Sum( spad, &((simulation_data *)data->d_simulation_data)->my_en.e_lp,
system->n );
- /* reduction for E_Ov */
Cuda_Reduction_Sum( &spad[system->n],
&((simulation_data *)data->d_simulation_data)->my_en.e_ov,
system->n );
- /* reduction for E_Un */
Cuda_Reduction_Sum( &spad[2 * system->n],
&((simulation_data *)data->d_simulation_data)->my_en.e_un,
system->n );
}
+#endif
compute_bonded_part1 = TRUE;
}
@@ -1869,7 +1894,8 @@ int Cuda_Compute_Bonded_Forces( reax_system *system, control_params *control,
"Cuda_Compute_Bonded_Forces::workspace->scratch" );
thbody = (int *) workspace->scratch;
- spad = (real *) workspace->scratch; /* in case scratch gets reallocated above, changing the pointer */
+ /* in case scratch gets reallocated above, reassign scratch pointer */
+ spad = (real *) workspace->scratch;
ret = Cuda_Estimate_Storage_Three_Body( system, control, data, workspace,
lists, thbody );
@@ -1878,32 +1904,49 @@ int Cuda_Compute_Bonded_Forces( reax_system *system, control_params *control,
{
Cuda_Init_Three_Body_Indices( thbody, system->total_thbodies_indices, lists );
+#if !defined(CUDA_ACCUM_ENERGY_ATOMIC)
cuda_memset( spad, 0,
(sizeof(real) * 3 + sizeof(rvec)) * system->N + sizeof(rvec) * control->blocks_n,
"Cuda_Compute_Bonded_Forces::spad" );
+#else
+ cuda_memset( &((simulation_data *)data->d_simulation_data)->my_en.e_ang,
+ 0, sizeof(real), "Cuda_Compute_Bonded_Forces::e_ang" );
+ cuda_memset( &((simulation_data *)data->d_simulation_data)->my_en.e_pen,
+ 0, sizeof(real), "Cuda_Compute_Bonded_Forces::e_pen" );
+ cuda_memset( &((simulation_data *)data->d_simulation_data)->my_en.e_coa,
+ 0, sizeof(real), "Cuda_Compute_Bonded_Forces::e_coa" );
+ cuda_memset( &((simulation_data *)data->d_simulation_data)->my_ext_press,
+ 0, sizeof(rvec), "Cuda_Compute_Bonded_Forces::my_ext_press" );
+#endif
Cuda_Valence_Angles_Part1 <<< control->blocks_n, control->block_size_n >>>
- ( system->d_my_atoms, system->reax_param.d_gp,
+ ( system->d_my_atoms, system->reax_param.d_gp,
system->reax_param.d_sbp, system->reax_param.d_thbp,
(control_params *) control->d_control_params,
*(workspace->d_workspace), *(lists[BONDS]), *(lists[THREE_BODIES]),
system->n, system->N, system->reax_param.num_atom_types,
- spad, &spad[system->N], &spad[2 * system->N], (rvec *) (&spad[3 * system->N]) );
+#if !defined(CUDA_ACCUM_ENERGY_ATOMIC)
+ spad, &spad[system->N], &spad[2 * system->N], (rvec *) (&spad[3 * system->N])
+#else
+ &((simulation_data *)data->d_simulation_data)->my_en.e_ang,
+ &((simulation_data *)data->d_simulation_data)->my_en.e_pen,
+ &((simulation_data *)data->d_simulation_data)->my_en.e_coa,
+ &((simulation_data *)data->d_simulation_data)->my_ext_press
+#endif
+ );
cudaCheckError( );
+#if !defined(CUDA_ACCUM_ENERGY_ATOMIC)
if ( update_energy == TRUE )
{
- /* reduction for E_Ang */
Cuda_Reduction_Sum( spad,
&((simulation_data *)data->d_simulation_data)->my_en.e_ang,
system->N );
- /* reduction for E_Pen */
Cuda_Reduction_Sum( &spad[system->N],
&((simulation_data *)data->d_simulation_data)->my_en.e_pen,
system->N );
- /* reduction for E_Coa */
Cuda_Reduction_Sum( &spad[2 * system->N],
&((simulation_data *)data->d_simulation_data)->my_en.e_coa,
system->N );
@@ -1913,7 +1956,6 @@ int Cuda_Compute_Bonded_Forces( reax_system *system, control_params *control,
{
rvec_spad = (rvec *) (&spad[3 * system->N]);
- /* reduction for ext_pres */
k_reduction_rvec <<< control->blocks_n, control->block_size_n,
sizeof(rvec) * (control->block_size_n / 32) >>>
( rvec_spad, &rvec_spad[system->N], system->N );
@@ -1929,6 +1971,7 @@ int Cuda_Compute_Bonded_Forces( reax_system *system, control_params *control,
// &((simulation_data *)data->d_simulation_data)->my_ext_press,
// system->N );
}
+#endif
#if !defined(CUDA_ACCUM_FORCE_ATOMIC)
Cuda_Valence_Angles_Part2 <<< control->blocks_n, control->block_size_n >>>
@@ -1938,25 +1981,40 @@ int Cuda_Compute_Bonded_Forces( reax_system *system, control_params *control,
#endif
/* 5. Torsion Angles Interactions */
- cuda_memset( spad, 0, (sizeof(real) * 2 + sizeof(rvec)) * system->n + sizeof(rvec) * control->blocks,
+#if !defined(CUDA_ACCUM_ENERGY_ATOMIC)
+ cuda_memset( spad, 0,(sizeof(real) * 2 + sizeof(rvec)) * system->n + sizeof(rvec) * control->blocks,
"Cuda_Compute_Bonded_Forces::spad" );
+#else
+ cuda_memset( &((simulation_data *)data->d_simulation_data)->my_en.e_tor,
+ 0, sizeof(real), "Cuda_Compute_Bonded_Forces::e_tor" );
+ cuda_memset( &((simulation_data *)data->d_simulation_data)->my_en.e_con,
+ 0, sizeof(real), "Cuda_Compute_Bonded_Forces::e_con" );
+ cuda_memset( &((simulation_data *)data->d_simulation_data)->my_ext_press,
+ 0, sizeof(rvec), "Cuda_Compute_Bonded_Forces::my_ext_press" );
+#endif
Cuda_Torsion_Angles_Part1 <<< control->blocks, control->block_size >>>
( system->d_my_atoms, system->reax_param.d_gp, system->reax_param.d_fbp,
(control_params *) control->d_control_params, *(lists[BONDS]),
*(lists[THREE_BODIES]), *(workspace->d_workspace), system->n,
system->reax_param.num_atom_types,
- spad, &spad[system->n], (rvec *) (&spad[2 * system->n]) );
+#if !defined(CUDA_ACCUM_ENERGY_ATOMIC)
+ spad, &spad[system->n], (rvec *) (&spad[2 * system->n])
+#else
+ &((simulation_data *)data->d_simulation_data)->my_en.e_tor,
+ &((simulation_data *)data->d_simulation_data)->my_en.e_con,
+ &((simulation_data *)data->d_simulation_data)->my_ext_press
+#endif
+ );
cudaCheckError( );
+#if !defined(CUDA_ACCUM_ENERGY_ATOMIC)
if ( update_energy == TRUE )
{
- /* reduction for E_Tor */
Cuda_Reduction_Sum( spad,
&((simulation_data *)data->d_simulation_data)->my_en.e_tor,
system->n );
- /* reduction for E_Con */
Cuda_Reduction_Sum( &spad[system->n],
&((simulation_data *)data->d_simulation_data)->my_en.e_con,
system->n );
@@ -1966,7 +2024,6 @@ int Cuda_Compute_Bonded_Forces( reax_system *system, control_params *control,
{
rvec_spad = (rvec *) (&spad[2 * system->n]);
- /* reduction for ext_pres */
k_reduction_rvec <<< control->blocks, control->block_size,
sizeof(rvec) * (control->block_size / 32) >>>
( rvec_spad, &rvec_spad[system->n], system->n );
@@ -1982,6 +2039,7 @@ int Cuda_Compute_Bonded_Forces( reax_system *system, control_params *control,
// &((simulation_data *)data->d_simulation_data)->my_ext_press,
// system->n );
}
+#endif
#if !defined(CUDA_ACCUM_FORCE_ATOMIC)
Cuda_Torsion_Angles_Part2 <<< control->blocks_n, control->block_size_n >>>
@@ -2014,7 +2072,6 @@ int Cuda_Compute_Bonded_Forces( reax_system *system, control_params *control,
if ( update_energy == TRUE )
{
- /* reduction for E_HB */
Cuda_Reduction_Sum( spad,
&((simulation_data *)data->d_simulation_data)->my_en.e_hb,
system->n );
@@ -2024,7 +2081,6 @@ int Cuda_Compute_Bonded_Forces( reax_system *system, control_params *control,
{
rvec_spad = (rvec *) (&spad[system->n]);
- /* reduction for ext_pres */
k_reduction_rvec <<< control->blocks, control->block_size,
sizeof(rvec) * (control->block_size / 32) >>>
( rvec_spad, &rvec_spad[system->n], system->n );
diff --git a/PG-PuReMD/src/cuda/cuda_multi_body.cu b/PG-PuReMD/src/cuda/cuda_multi_body.cu
index 67f49c3d..7969ae7d 100644
--- a/PG-PuReMD/src/cuda/cuda_multi_body.cu
+++ b/PG-PuReMD/src/cuda/cuda_multi_body.cu
@@ -30,13 +30,16 @@
CUDA_GLOBAL void Cuda_Atom_Energy_Part1( reax_atom *my_atoms, global_parameters gp,
single_body_parameters *sbp, two_body_parameters *tbp,
storage workspace, reax_list bond_list, int n, int num_atom_types,
- real *data_e_lp, real *dat_e_ov, real *data_e_un )
+ real *e_lp_g, real *e_ov_g, real *e_un_g )
{
int i, j, pj, type_i, type_j;
real Delta_lpcorr, dfvl;
- real e_lp, expvd2, inv_expvd2, dElp, CElp, DlpVi;
- real e_lph, Di, vov3, deahu2dbo, deahu2dsbo;
- real e_ov, CEover1, CEover2, CEover3, CEover4;
+ real expvd2, inv_expvd2, dElp, CElp, DlpVi;
+ real Di, vov3, deahu2dbo, deahu2dsbo;
+ real CEover1, CEover2, CEover3, CEover4;
+#if defined(CUDA_ACCUM_ENERGY_ATOMIC)
+ real e_lp_l;
+#endif
real exp_ovun1, exp_ovun2, sum_ovun1, sum_ovun2;
real exp_ovun2n, exp_ovun6, exp_ovun8;
real inv_exp_ovun1, inv_exp_ovun2, inv_exp_ovun2n, inv_exp_ovun8;
@@ -71,8 +74,11 @@ CUDA_GLOBAL void Cuda_Atom_Energy_Part1( reax_atom *my_atoms, global_parameters
inv_expvd2 = 1.0 / (1.0 + expvd2 );
/* calculate the energy */
- e_lp = p_lp2 * workspace.Delta_lp[i] * inv_expvd2;
- data_e_lp[i] += e_lp;
+#if !defined(CUDA_ACCUM_ENERGY_ATOMIC)
+ e_lp_g[i] += p_lp2 * workspace.Delta_lp[i] * inv_expvd2;
+#else
+ e_lp_l = p_lp2 * workspace.Delta_lp[i] * inv_expvd2;
+#endif
dElp = p_lp2 * inv_expvd2 + 75.0 * p_lp2 * workspace.Delta_lp[i]
* expvd2 * SQR(inv_expvd2);
@@ -80,14 +86,6 @@ CUDA_GLOBAL void Cuda_Atom_Energy_Part1( reax_atom *my_atoms, global_parameters
workspace.CdDelta[i] += CElp; // lp - 1st term
-#if defined(TEST_ENERGY)
- fprintf( out_control->elp, "%23.15e%23.15e%23.15e%23.15e\n",
- p_lp2, workspace.Delta_lp_temp[i], expvd2, dElp );
- fprintf( out_control->elp, "%6d%12.4f%12.4f%12.4f\n",
- system->my_atoms[i].orig_id, workspace.nlp[i],
- e_lp, data->my_en.e_lp );
-#endif
-
#if defined(TEST_FORCES)
Add_dDelta( system, lists, i, CElp, workspace.f_lp ); // lp - 1st term
#endif
@@ -115,8 +113,11 @@ CUDA_GLOBAL void Cuda_Atom_Energy_Part1( reax_atom *my_atoms, global_parameters
if ( vov3 > 3.0 )
{
- e_lph = p_lp3 * SQR( vov3 - 3.0 );
- data_e_lp[i] += e_lph;
+#if !defined(CUDA_ACCUM_ENERGY_ATOMIC)
+ e_lp_g[i] += p_lp3 * SQR( vov3 - 3.0 );
+#else
+ e_lp_l += p_lp3 * SQR( vov3 - 3.0 );
+#endif
deahu2dbo = 2.0 * p_lp3 * (vov3 - 3.0);
deahu2dsbo = 2.0 * p_lp3 * (vov3 - 3.0)
@@ -124,25 +125,18 @@ CUDA_GLOBAL void Cuda_Atom_Energy_Part1( reax_atom *my_atoms, global_parameters
bo_ij->Cdbo += deahu2dbo;
workspace.CdDelta[i] += deahu2dsbo;
-
-#if defined(TEST_ENERGY)
- fprintf( out_control->elp,"C2cor%6d%6d%12.6f%12.6f%12.6f\n",
- system->my_atoms[i].orig_id, system->my_atoms[j].orig_id,
- e_lph, deahu2dbo, deahu2dsbo );
-#endif
-
-#if defined(TEST_FORCES)
- Add_dBO( system, lists, i, pj, deahu2dbo, workspace.f_lp );
- Add_dDelta( system, lists, i, deahu2dsbo, workspace.f_lp );
-#endif
}
}
}
}
}
+#if defined(CUDA_ACCUM_ENERGY_ATOMIC)
+ atomicAdd( (double *) e_lp_g, (double) e_lp_l );
+#endif
+
/* over-coordination energy */
- if( sbp_i->mass > 21.0 )
+ if ( sbp_i->mass > 21.0 )
{
dfvl = 0.0;
}
@@ -179,8 +173,11 @@ CUDA_GLOBAL void Cuda_Atom_Energy_Part1( reax_atom *my_atoms, global_parameters
DlpVi = 1.0 / (Delta_lpcorr + sbp_i->valency + 1.0e-8);
CEover1 = Delta_lpcorr * DlpVi * inv_exp_ovun2;
- e_ov = sum_ovun1 * CEover1;
- dat_e_ov[i] += e_ov;
+#if !defined(CUDA_ACCUM_ENERGY_ATOMIC)
+ e_ov_g[i] += sum_ovun1 * CEover1;
+#else
+ atomicAdd( (double *) e_ov_g, (double) (sum_ovun1 * CEover1) );
+#endif
CEover2 = sum_ovun1 * DlpVi * inv_exp_ovun2 * (1.0 - Delta_lpcorr
* ( DlpVi + p_ovun2 * exp_ovun2 * inv_exp_ovun2 ));
@@ -201,7 +198,11 @@ CUDA_GLOBAL void Cuda_Atom_Energy_Part1( reax_atom *my_atoms, global_parameters
inv_exp_ovun8 = 1.0 / (1.0 + exp_ovun8);
e_un = -p_ovun5 * (1.0 - exp_ovun6) * inv_exp_ovun2n * inv_exp_ovun8;
- data_e_un[i] += e_un;
+#if !defined(CUDA_ACCUM_ENERGY_ATOMIC)
+ e_un_g[i] += e_un;
+#else
+ atomicAdd( (double *) e_un_g, (double) e_un );
+#endif
CEunder1 = inv_exp_ovun2n * ( p_ovun5 * p_ovun6 * exp_ovun6 * inv_exp_ovun8
+ p_ovun2 * e_un * exp_ovun2n );
@@ -302,23 +303,6 @@ CUDA_GLOBAL void Cuda_Atom_Energy_Part1( reax_atom *my_atoms, global_parameters
workspace.f_un, workspace.f_un ); // UnCoor - 2b
#endif
}
-
-#if defined(TEST_ENERGY)
- //fprintf( out_control->elp, "%6d%24.15e%24.15e%24.15e\n",
- //fprintf( out_control->elp, "%6d%12.4f%12.4f%12.4f\n",
- // system->my_atoms[i].orig_id, workspace.nlp[i],
- // e_lp, data->my_en.e_lp );
-
- //fprintf( out_control->eov, "%6d%24.15e%24.15e\n",
- fprintf( out_control->eov, "%6d%12.4f%12.4f\n",
- system->my_atoms[i].orig_id,
- e_ov, data->my_en.e_ov + data->my_en.e_un );
-
- //fprintf( out_control->eun, "%6d%24.15e%24.15e\n",
- fprintf( out_control->eun, "%6d%12.4f%12.4f\n",
- system->my_atoms[i].orig_id,
- e_un, data->my_en.e_ov + data->my_en.e_un );
-#endif
}
diff --git a/PG-PuReMD/src/cuda/cuda_torsion_angles.cu b/PG-PuReMD/src/cuda/cuda_torsion_angles.cu
index e0e10fe2..f9648c36 100644
--- a/PG-PuReMD/src/cuda/cuda_torsion_angles.cu
+++ b/PG-PuReMD/src/cuda/cuda_torsion_angles.cu
@@ -144,7 +144,7 @@ CUDA_DEVICE static real Calculate_Omega( const rvec dvec_ij, real r_ij, const rv
CUDA_GLOBAL void Cuda_Torsion_Angles_Part1( reax_atom *my_atoms, global_parameters gp,
four_body_header *d_fbp, control_params *control, reax_list bond_list,
reax_list thb_list, storage workspace, int n, int num_atom_types,
- real *data_e_tor, real *data_e_con, rvec *data_ext_press )
+ real *e_tor_g, real *e_con_g, rvec *ext_press_g )
{
int i, j, k, l, pi, pj, pk, pl, pij, plk;
int type_i, type_j, type_k, type_l;
@@ -170,9 +170,14 @@ CUDA_GLOBAL void Cuda_Torsion_Angles_Part1( reax_atom *my_atoms, global_paramete
real CEtors5, CEtors6, CEtors7, CEtors8, CEtors9;
real Cconj, CEconj1, CEconj2, CEconj3;
real CEconj4, CEconj5, CEconj6;
- real e_tor, e_con;
+#if defined(CUDA_ACCUM_ENERGY_ATOMIC)
+ real e_tor_l, e_con_l;
+#endif
rvec dvec_li;
rvec force, ext_press;
+#if defined(CUDA_ACCUM_ENERGY_ATOMIC)
+ rvec ext_press_l;
+#endif
ivec rel_box_jl;
// rtensor total_rtensor, temp_rtensor;
four_body_header *fbh;
@@ -193,6 +198,11 @@ CUDA_GLOBAL void Cuda_Torsion_Angles_Part1( reax_atom *my_atoms, global_paramete
p_tor3 = gp.l[24];
p_tor4 = gp.l[25];
p_cot2 = gp.l[27];
+#if defined(CUDA_ACCUM_ENERGY_ATOMIC)
+ e_tor_l = 0.0;
+ e_con_l = 0.0;
+ rvec_MakeZero( ext_press_l );
+#endif
#if defined(DEBUG_FOCUS)
num_frb_intrs = 0;
#endif
@@ -349,8 +359,11 @@ CUDA_GLOBAL void Cuda_Torsion_Angles_Part1( reax_atom *my_atoms, global_paramete
// + fbp->V2 * exp_tor1 * (1.0 - SQR(cos_omega))
// + fbp->V3 * (0.5 + 2.0 * CUBE(cos_omega) - 1.5 * cos_omega);
- e_tor = fn10 * sin_ijk * sin_jkl * CV;
- data_e_tor[j] += e_tor;
+#if !defined(CUDA_ACCUM_ENERGY_ATOMIC)
+ e_tor_g[j] += fn10 * sin_ijk * sin_jkl * CV;
+#else
+ e_tor_l += fn10 * sin_ijk * sin_jkl * CV;
+#endif
dfn11 = (-p_tor3 * exp_tor3_DjDk
+ (p_tor3 * exp_tor3_DjDk - p_tor4 * exp_tor4_DjDk)
@@ -386,9 +399,13 @@ CUDA_GLOBAL void Cuda_Torsion_Angles_Part1( reax_atom *my_atoms, global_paramete
/* 4-body conjugation energy */
fn12 = exp_cot2_ij * exp_cot2_jk * exp_cot2_kl;
- e_con = fbp->p_cot1 * fn12
+#if !defined(CUDA_ACCUM_ENERGY_ATOMIC)
+ e_con_g[j] += fbp->p_cot1 * fn12
* (1.0 + (SQR(cos_omega) - 1.0) * sin_ijk * sin_jkl);
- data_e_con[j] += e_con;
+#else
+ e_con_l += fbp->p_cot1 * fn12
+ * (1.0 + (SQR(cos_omega) - 1.0) * sin_ijk * sin_jkl);
+#endif
Cconj = -2.0 * fn12 * fbp->p_cot1 * p_cot2
* (1.0 + (SQR(cos_omega) - 1.0) * sin_ijk * sin_jkl);
@@ -491,7 +508,11 @@ CUDA_GLOBAL void Cuda_Torsion_Angles_Part1( reax_atom *my_atoms, global_paramete
rvec_Scale( force, CEtors7 + CEconj4, p_ijk->dcos_dk );
atomic_rvecAdd( pbond_ij->ta_f, force );
rvec_iMultiply( ext_press, pbond_ij->rel_box, force );
- rvec_Add( data_ext_press[j], ext_press );
+#if !defined(CUDA_ACCUM_ENERGY_ATOMIC)
+ rvec_Add( ext_press_g[j], ext_press );
+#else
+ rvec_Add( ext_press_l, ext_press );
+#endif
rvec_ScaledAdd( workspace.f[j],
CEtors7 + CEconj4, p_ijk->dcos_dj );
@@ -499,7 +520,11 @@ CUDA_GLOBAL void Cuda_Torsion_Angles_Part1( reax_atom *my_atoms, global_paramete
rvec_Scale( force, CEtors7 + CEconj4, p_ijk->dcos_di );
atomic_rvecAdd( pbond_jk->ta_f, force );
rvec_iMultiply( ext_press, pbond_jk->rel_box, force );
- rvec_Add( data_ext_press[j], ext_press );
+#if !defined(CUDA_ACCUM_ENERGY_ATOMIC)
+ rvec_Add( ext_press_g[j], ext_press );
+#else
+ rvec_Add( ext_press_l, ext_press );
+#endif
/* dcos_theta_jkl */
rvec_ScaledAdd( workspace.f[j],
@@ -508,18 +533,30 @@ CUDA_GLOBAL void Cuda_Torsion_Angles_Part1( reax_atom *my_atoms, global_paramete
rvec_Scale( force, CEtors8 + CEconj5, p_jkl->dcos_dj );
atomic_rvecAdd( pbond_jk->ta_f, force );
rvec_iMultiply( ext_press, pbond_jk->rel_box, force );
- rvec_Add( data_ext_press[j], ext_press );
+#if !defined(CUDA_ACCUM_ENERGY_ATOMIC)
+ rvec_Add( ext_press_g[j], ext_press );
+#else
+ rvec_Add( ext_press_l, ext_press );
+#endif
rvec_Scale( force, CEtors8 + CEconj5, p_jkl->dcos_dk );
rvec_Add( pbond_kl->ta_f, force );
rvec_iMultiply( ext_press, rel_box_jl, force );
- rvec_Add( data_ext_press[j], ext_press );
+#if !defined(CUDA_ACCUM_ENERGY_ATOMIC)
+ rvec_Add( ext_press_g[j], ext_press );
+#else
+ rvec_Add( ext_press_l, ext_press );
+#endif
/* dcos_omega */
rvec_Scale( force, CEtors9 + CEconj6, dcos_omega_di );
atomic_rvecAdd( pbond_ij->ta_f, force );
rvec_iMultiply( ext_press, pbond_ij->rel_box, force );
- rvec_Add( data_ext_press[j], ext_press );
+#if !defined(CUDA_ACCUM_ENERGY_ATOMIC)
+ rvec_Add( ext_press_g[j], ext_press );
+#else
+ rvec_Add( ext_press_l, ext_press );
+#endif
rvec_ScaledAdd( workspace.f[j],
CEtors9 + CEconj6, dcos_omega_dj );
@@ -527,12 +564,20 @@ CUDA_GLOBAL void Cuda_Torsion_Angles_Part1( reax_atom *my_atoms, global_paramete
rvec_Scale( force, CEtors9 + CEconj6, dcos_omega_dk );
rvec_Add( pbond_jk->ta_f, force );
rvec_iMultiply( ext_press, pbond_jk->rel_box, force );
- rvec_Add( data_ext_press[j], ext_press );
+#if !defined(CUDA_ACCUM_ENERGY_ATOMIC)
+ rvec_Add( ext_press_g[j], ext_press );
+#else
+ rvec_Add( ext_press_l, ext_press );
+#endif
rvec_Scale( force, CEtors9 + CEconj6, dcos_omega_dl );
rvec_Add( pbond_kl->ta_f, force );
rvec_iMultiply( ext_press, rel_box_jl, force );
- rvec_Add( data_ext_press[j], ext_press );
+#if !defined(CUDA_ACCUM_ENERGY_ATOMIC)
+ rvec_Add( ext_press_g[j], ext_press );
+#else
+ rvec_Add( ext_press_l, ext_press );
+#endif
#else
ivec_Sum( rel_box_jl, pbond_jk->rel_box, pbond_kl->rel_box );
@@ -540,7 +585,11 @@ CUDA_GLOBAL void Cuda_Torsion_Angles_Part1( reax_atom *my_atoms, global_paramete
rvec_Scale( force, CEtors7 + CEconj4, p_ijk->dcos_dk );
atomic_rvecAdd( workspace.f[i], force );
rvec_iMultiply( ext_press, pbond_ij->rel_box, force );
- rvec_Add( data_ext_press[j], ext_press );
+#if !defined(CUDA_ACCUM_ENERGY_ATOMIC)
+ rvec_Add( ext_press_g[j], ext_press );
+#else
+ rvec_Add( ext_press_l, ext_press );
+#endif
atomic_rvecScaledAdd( workspace.f[j],
CEtors7 + CEconj4, p_ijk->dcos_dj );
@@ -548,7 +597,11 @@ CUDA_GLOBAL void Cuda_Torsion_Angles_Part1( reax_atom *my_atoms, global_paramete
rvec_Scale( force, CEtors7 + CEconj4, p_ijk->dcos_di );
atomic_rvecAdd( workspace.f[k], force );
rvec_iMultiply( ext_press, pbond_jk->rel_box, force );
- rvec_Add( data_ext_press[j], ext_press );
+#if !defined(CUDA_ACCUM_ENERGY_ATOMIC)
+ rvec_Add( ext_press_g[j], ext_press );
+#else
+ rvec_Add( ext_press_l, ext_press );
+#endif
/* dcos_theta_jkl */
atomic_rvecScaledAdd( workspace.f[j],
@@ -557,18 +610,30 @@ CUDA_GLOBAL void Cuda_Torsion_Angles_Part1( reax_atom *my_atoms, global_paramete
rvec_Scale( force, CEtors8 + CEconj5, p_jkl->dcos_dj );
atomic_rvecAdd( workspace.f[k], force );
rvec_iMultiply( ext_press, pbond_jk->rel_box, force );
- rvec_Add( data_ext_press[j], ext_press );
+#if !defined(CUDA_ACCUM_ENERGY_ATOMIC)
+ rvec_Add( ext_press_g[j], ext_press );
+#else
+ rvec_Add( ext_press_l, ext_press );
+#endif
rvec_Scale( force, CEtors8 + CEconj5, p_jkl->dcos_dk );
atomic_rvecAdd( workspace.f[l], force );
rvec_iMultiply( ext_press, rel_box_jl, force );
- rvec_Add( data_ext_press[j], ext_press );
+#if !defined(CUDA_ACCUM_ENERGY_ATOMIC)
+ rvec_Add( ext_press_g[j], ext_press );
+#else
+ rvec_Add( ext_press_l, ext_press );
+#endif
/* dcos_omega */
rvec_Scale( force, CEtors9 + CEconj6, dcos_omega_di );
atomic_rvecAdd( workspace.f[i], force );
rvec_iMultiply( ext_press, pbond_ij->rel_box, force );
- rvec_Add( data_ext_press[j], ext_press );
+#if !defined(CUDA_ACCUM_ENERGY_ATOMIC)
+ rvec_Add( ext_press_g[j], ext_press );
+#else
+ rvec_Add( ext_press_l, ext_press );
+#endif
atomic_rvecScaledAdd( workspace.f[j],
CEtors9 + CEconj6, dcos_omega_dj );
@@ -576,111 +641,22 @@ CUDA_GLOBAL void Cuda_Torsion_Angles_Part1( reax_atom *my_atoms, global_paramete
rvec_Scale( force, CEtors9 + CEconj6, dcos_omega_dk );
atomic_rvecAdd( workspace.f[k], force );
rvec_iMultiply( ext_press, pbond_jk->rel_box, force );
- rvec_Add( data_ext_press[j], ext_press );
+#if !defined(CUDA_ACCUM_ENERGY_ATOMIC)
+ rvec_Add( ext_press_g[j], ext_press );
+#else
+ rvec_Add( ext_press_l, ext_press );
+#endif
rvec_Scale( force, CEtors9 + CEconj6, dcos_omega_dl );
rvec_Add( workspace.f[l], force );
rvec_iMultiply( ext_press, rel_box_jl, force );
- rvec_Add( data_ext_press[j], ext_press );
-#endif
- }
-
-#if defined(TEST_ENERGY)
- /* fprintf( out_control->etor,
- "%12.8f%12.8f%12.8f%12.8f%12.8f%12.8f%12.8f\n",
- r_ij, r_jk, r_kl, cos_ijk, cos_jkl, sin_ijk, sin_jkl );
- fprintf( out_control->etor, "%12.8f\n", dfn11 ); */
- /* fprintf( out_control->etor,
- "%12.8f%12.8f%12.8f%12.8f%12.8f%12.8f%12.8f%12.8f\n",
- CEtors2, CEtors3, CEtors4, CEtors5, CEtors6,
- CEtors7, CEtors8, CEtors9 ); */
- /* fprintf( out_control->etor,
- "%12.8f%12.8f%12.8f%12.8f%12.8f%12.8f%12.8f%12.8f\n",
- htra, htrb, htrc, hthd, hthe, hnra, hnrc, hnhd, hnhe ); */
- /* fprintf( out_control->etor,
- "%12.8f%12.8f%12.8f%12.8f%12.8f%12.8f\n",
- CEconj1, CEconj2, CEconj3, CEconj4, CEconj5, CEconj6 ); */
-
- /* fprintf( out_control->etor, "%12.6f%12.6f%12.6f%12.6f\n",
- fbp->V1, fbp->V2, fbp->V3, fbp->p_tor1 );*/
-
- fprintf(out_control->etor,
- //"%6d%6d%6d%6d%24.15e%24.15e%24.15e%24.15e\n",
- "%6d%6d%6d%6d%12.4f%12.4f%12.4f%12.4f\n",
- system->my_atoms[i].orig_id,system->my_atoms[j].orig_id,
- system->my_atoms[k].orig_id,system->my_atoms[l].orig_id,
- RAD2DEG(omega), BOA_jk, e_tor, data->my_en.e_tor );
-
- fprintf(out_control->econ,
- //"%6d%6d%6d%6d%24.15e%24.15e%24.15e%24.15e%24.15e%24.15e\n",
- "%6d%6d%6d%6d%12.4f%12.4f%12.4f%12.4f%12.4f%12.4f\n",
- system->my_atoms[i].orig_id,system->my_atoms[j].orig_id,
- system->my_atoms[k].orig_id,system->my_atoms[l].orig_id,
- RAD2DEG(omega), BOA_ij, BOA_jk, BOA_kl,
- e_con, data->my_en.e_con );
+#if !defined(CUDA_ACCUM_ENERGY_ATOMIC)
+ rvec_Add( ext_press_g[j], ext_press );
+#else
+ rvec_Add( ext_press_l, ext_press );
#endif
-
-#if defined(TEST_FORCES)
- /* Torsion Forces */
- Add_dBOpinpi2( system, lists, j, pk, CEtors2, 0.0,
- workspace.f_tor, workspace.f_tor );
- Add_dDelta( system, lists, j, CEtors3, workspace.f_tor );
- Add_dDelta( system, lists, k, CEtors3, workspace.f_tor );
- Add_dBO( system, lists, j, pij, CEtors4, workspace.f_tor );
- Add_dBO( system, lists, j, pk, CEtors5, workspace.f_tor );
- Add_dBO( system, lists, k, plk, CEtors6, workspace.f_tor );
-
- rvec_ScaledAdd( workspace.f_tor[i],
- CEtors7, p_ijk->dcos_dk );
- rvec_ScaledAdd( workspace.f_tor[j],
- CEtors7, p_ijk->dcos_dj );
- rvec_ScaledAdd( workspace.f_tor[k],
- CEtors7, p_ijk->dcos_di );
-
- rvec_ScaledAdd( workspace.f_tor[j],
- CEtors8, p_jkl->dcos_di );
- rvec_ScaledAdd( workspace.f_tor[k],
- CEtors8, p_jkl->dcos_dj );
- rvec_ScaledAdd( workspace.f_tor[l],
- CEtors8, p_jkl->dcos_dk );
-
- rvec_ScaledAdd( workspace.f_tor[i],
- CEtors9, dcos_omega_di );
- rvec_ScaledAdd( workspace.f_tor[j],
- CEtors9, dcos_omega_dj );
- rvec_ScaledAdd( workspace.f_tor[k],
- CEtors9, dcos_omega_dk );
- rvec_ScaledAdd( workspace.f_tor[l],
- CEtors9, dcos_omega_dl );
-
- /* Conjugation Forces */
- Add_dBO( system, lists, j, pij, CEconj1, workspace.f_con );
- Add_dBO( system, lists, j, pk, CEconj2, workspace.f_con );
- Add_dBO( system, lists, k, plk, CEconj3, workspace.f_con );
-
- rvec_ScaledAdd( workspace.f_con[i],
- CEconj4, p_ijk->dcos_dk );
- rvec_ScaledAdd( workspace.f_con[j],
- CEconj4, p_ijk->dcos_dj );
- rvec_ScaledAdd( workspace.f_con[k],
- CEconj4, p_ijk->dcos_di );
-
- rvec_ScaledAdd( workspace.f_con[j],
- CEconj5, p_jkl->dcos_di );
- rvec_ScaledAdd( workspace.f_con[k],
- CEconj5, p_jkl->dcos_dj );
- rvec_ScaledAdd( workspace.f_con[l],
- CEconj5, p_jkl->dcos_dk );
-
- rvec_ScaledAdd( workspace.f_con[i],
- CEconj6, dcos_omega_di );
- rvec_ScaledAdd( workspace.f_con[j],
- CEconj6, dcos_omega_dj );
- rvec_ScaledAdd( workspace.f_con[k],
- CEconj6, dcos_omega_dk );
- rvec_ScaledAdd( workspace.f_con[l],
- CEconj6, dcos_omega_dl );
#endif
+ }
} // pl check ends
} // pl loop ends
} // pi check ends
@@ -689,6 +665,12 @@ CUDA_GLOBAL void Cuda_Torsion_Angles_Part1( reax_atom *my_atoms, global_paramete
} // j<k && j-k neighbor check ends
} // pk loop ends
// } // j loop
+
+#if defined(CUDA_ACCUM_ENERGY_ATOMIC)
+ atomicAdd( (double *) e_tor_g, (double) e_tor_l );
+ atomicAdd( (double *) e_con_g, (double) e_con_l );
+ atomic_rvecAdd( *ext_press_g, ext_press_l );
+#endif
}
diff --git a/PG-PuReMD/src/cuda/cuda_valence_angles.cu b/PG-PuReMD/src/cuda/cuda_valence_angles.cu
index 32ac5543..df1583ab 100644
--- a/PG-PuReMD/src/cuda/cuda_valence_angles.cu
+++ b/PG-PuReMD/src/cuda/cuda_valence_angles.cu
@@ -36,7 +36,7 @@ CUDA_GLOBAL void Cuda_Valence_Angles_Part1( reax_atom *my_atoms,
global_parameters gp, single_body_parameters *sbp, three_body_header *d_thbh,
control_params *control, storage workspace, reax_list bond_list,
reax_list thb_list, int n, int N, int num_atom_types,
- real *data_e_ang, real *data_e_pen, real *data_e_coa, rvec *my_ext_press )
+ real *e_ang_g, real *e_pen_g, real *e_coa_g, rvec *ext_press_g )
{
int i, j, pi, k, pk, t;
int type_i, type_j, type_k;
@@ -53,13 +53,19 @@ CUDA_GLOBAL void Cuda_Valence_Angles_Part1( reax_atom *my_atoms,
real dSBO1, dSBO2, SBO, SBO2, CSBO2, SBOp, prod_SBO, vlpadj;
real CEval1, CEval2, CEval3, CEval4, CEval5, CEval6, CEval7, CEval8;
real CEpen1, CEpen2, CEpen3;
- real e_ang, e_coa, e_pen;
+ real e_pen, e_coa;
+#if defined(CUDA_ACCUM_ENERGY_ATOMIC)
+ real e_ang_l, e_coa_l, e_pen_l;
+#endif
real CEcoa1, CEcoa2, CEcoa3, CEcoa4, CEcoa5;
real Cf7ij, Cf7jk, Cf8j, Cf9j;
real f7_ij, f7_jk, f8_Dj, f9_Dj;
real Ctheta_0, theta_0, theta_00, theta, cos_theta, sin_theta;
real BOA_ij, BOA_jk;
rvec force, ext_press;
+#if defined(CUDA_ACCUM_ENERGY_ATOMIC)
+ rvec ext_press_l;
+#endif
three_body_header *thbh;
three_body_parameters *thbp;
three_body_interaction_data *p_ijk;
@@ -85,12 +91,19 @@ CUDA_GLOBAL void Cuda_Valence_Angles_Part1( reax_atom *my_atoms,
p_val9 = gp.l[16];
p_val10 = gp.l[17];
//num_thb_intrs = j * THREE_BODY_OFFSET;
+#if defined(CUDA_ACCUM_ENERGY_ATOMIC)
+ e_ang_l = 0.0;
+ e_coa_l = 0.0;
+ e_pen_l = 0.0;
+ rvec_MakeZero( ext_press_l );
+#endif
type_j = my_atoms[j].type;
start_j = Start_Index( j, &bond_list );
end_j = End_Index( j, &bond_list );
p_val3 = sbp[ type_j ].p_val3;
p_val5 = sbp[ type_j ].p_val5;
+
/* sum of pi and pi-pi BO terms for all neighbors of atom j,
* used in determining the equilibrium angle between i-j-k */
SBOp = 0.0;
@@ -101,7 +114,7 @@ CUDA_GLOBAL void Cuda_Valence_Angles_Part1( reax_atom *my_atoms,
for ( t = start_j; t < end_j; ++t )
{
bo_jt = &bond_list.bond_list[t].bo_data;
- SBOp += (bo_jt->BO_pi + bo_jt->BO_pi2);
+ SBOp += bo_jt->BO_pi + bo_jt->BO_pi2;
temp = SQR( bo_jt->BO );
temp *= temp;
temp *= temp;
@@ -236,309 +249,239 @@ CUDA_GLOBAL void Cuda_Valence_Angles_Part1( reax_atom *my_atoms,
/* Fortran ReaxFF code hard-codes the constant below
* as of 2019-02-27, so use that for now */
- if ( j < n && BOA_jk >= 0.0 && (bo_ij->BO * bo_jk->BO) >= 0.00001 )
-// if ( j < n && BOA_jk >= 0.0 && (bo_ij->BO * bo_jk->BO) > SQR(control->thb_cut) )
+ if ( j >= n || BOA_jk < 0.0 || (bo_ij->BO * bo_jk->BO) < 0.00001 )
+// if ( j >= n || BOA_jk < 0.0 || (bo_ij->BO * bo_jk->BO) < SQR(control->thb_cut) )
{
- thbh = &d_thbh[
- index_thbp(type_i, type_j, type_k, num_atom_types) ];
+ continue;
+ }
+
+ thbh = &d_thbh[
+ index_thbp(type_i, type_j, type_k, num_atom_types) ];
- for ( cnt = 0; cnt < thbh->cnt; ++cnt )
+ for ( cnt = 0; cnt < thbh->cnt; ++cnt )
+ {
+ /* valence angle does not exist in the force field */
+ if ( FABS(thbh->prm[cnt].p_val1) < 0.001 )
{
- /* valence angle does not exist in the force field */
- if ( FABS(thbh->prm[cnt].p_val1) < 0.001 )
- {
- continue;
- }
+ continue;
+ }
- thbp = &thbh->prm[cnt];
-
- /* calculate valence angle energy */
- p_val1 = thbp->p_val1;
- p_val2 = thbp->p_val2;
- p_val4 = thbp->p_val4;
- p_val7 = thbp->p_val7;
- theta_00 = thbp->theta_00;
-
- exp3ij = EXP( -p_val3 * POW( BOA_ij, p_val4 ) );
- f7_ij = 1.0 - exp3ij;
- Cf7ij = p_val3 * p_val4
- * POW( BOA_ij, p_val4 - 1.0 ) * exp3ij;
-
- exp3jk = EXP( -p_val3 * POW( BOA_jk, p_val4 ) );
- f7_jk = 1.0 - exp3jk;
- Cf7jk = p_val3 * p_val4
- * POW( BOA_jk, p_val4 - 1.0 ) * exp3jk;
-
- expval7 = EXP( -p_val7 * workspace.Delta_boc[j] );
- trm8 = 1.0 + expval6 + expval7;
- f8_Dj = p_val5 - ( (p_val5 - 1.0) * (2.0 + expval6) / trm8 );
- Cf8j = ( (1.0 - p_val5) / SQR(trm8) )
- * (p_val6 * expval6 * trm8
- - (2.0 + expval6) * ( p_val6*expval6 - p_val7*expval7) );
-
- theta_0 = 180.0 - theta_00 * (1.0 - EXP(-p_val10 * (2.0 - SBO2)));
- theta_0 = DEG2RAD( theta_0 );
-
- expval2theta = p_val1 * EXP(-p_val2 * SQR(theta_0 - theta));
- if ( p_val1 >= 0.0 )
- {
- expval12theta = p_val1 - expval2theta;
- }
- /* to avoid linear Me-H-Me angles (6/6/06) */
- else
- {
- expval12theta = -expval2theta;
- }
+ thbp = &thbh->prm[cnt];
+
+ /* calculate valence angle energy */
+ p_val1 = thbp->p_val1;
+ p_val2 = thbp->p_val2;
+ p_val4 = thbp->p_val4;
+ p_val7 = thbp->p_val7;
+ theta_00 = thbp->theta_00;
+
+ exp3ij = EXP( -p_val3 * POW( BOA_ij, p_val4 ) );
+ f7_ij = 1.0 - exp3ij;
+ Cf7ij = p_val3 * p_val4
+ * POW( BOA_ij, p_val4 - 1.0 ) * exp3ij;
+
+ exp3jk = EXP( -p_val3 * POW( BOA_jk, p_val4 ) );
+ f7_jk = 1.0 - exp3jk;
+ Cf7jk = p_val3 * p_val4
+ * POW( BOA_jk, p_val4 - 1.0 ) * exp3jk;
+
+ expval7 = EXP( -p_val7 * workspace.Delta_boc[j] );
+ trm8 = 1.0 + expval6 + expval7;
+ f8_Dj = p_val5 - (p_val5 - 1.0) * (2.0 + expval6) / trm8;
+ Cf8j = ( (1.0 - p_val5) / SQR(trm8) )
+ * (p_val6 * expval6 * trm8
+ - (2.0 + expval6) * ( p_val6 * expval6 - p_val7 * expval7) );
+
+ theta_0 = 180.0 - theta_00 * (1.0 - EXP(-p_val10 * (2.0 - SBO2)));
+ theta_0 = DEG2RAD( theta_0 );
+
+ expval2theta = p_val1 * EXP(-p_val2 * SQR(theta_0 - theta));
+ if ( p_val1 >= 0.0 )
+ {
+ expval12theta = p_val1 - expval2theta;
+ }
+ /* to avoid linear Me-H-Me angles (6/6/06) */
+ else
+ {
+ expval12theta = -expval2theta;
+ }
- CEval1 = Cf7ij * f7_jk * f8_Dj * expval12theta;
- CEval2 = Cf7jk * f7_ij * f8_Dj * expval12theta;
- CEval3 = Cf8j * f7_ij * f7_jk * expval12theta;
- CEval4 = 2.0 * p_val2 * f7_ij * f7_jk * f8_Dj
- * expval2theta * (theta_0 - theta);
+ CEval1 = Cf7ij * f7_jk * f8_Dj * expval12theta;
+ CEval2 = Cf7jk * f7_ij * f8_Dj * expval12theta;
+ CEval3 = Cf8j * f7_ij * f7_jk * expval12theta;
+ CEval4 = 2.0 * p_val2 * f7_ij * f7_jk * f8_Dj
+ * expval2theta * (theta_0 - theta);
- Ctheta_0 = p_val10 * DEG2RAD(theta_00)
- * EXP( -p_val10 * (2.0 - SBO2) );
+ Ctheta_0 = p_val10 * DEG2RAD(theta_00)
+ * EXP( -p_val10 * (2.0 - SBO2) );
- CEval5 = CEval4 * Ctheta_0 * CSBO2;
- CEval6 = CEval5 * dSBO1;
- CEval7 = CEval5 * dSBO2;
- CEval8 = CEval4 / sin_theta;
+ CEval5 = CEval4 * Ctheta_0 * CSBO2;
+ CEval6 = CEval5 * dSBO1;
+ CEval7 = CEval5 * dSBO2;
+ CEval8 = CEval4 / sin_theta;
- if ( pk < pi )
- {
- e_ang = f7_ij * f7_jk * f8_Dj * expval12theta;
- data_e_ang[j] += e_ang;
- }
+ if ( pk < pi )
+ {
+#if !defined(CUDA_ACCUM_ENERGY_ATOMIC)
+ e_ang_g[j] += f7_ij * f7_jk * f8_Dj * expval12theta;
+#else
+ e_ang_l += f7_ij * f7_jk * f8_Dj * expval12theta;
+#endif
+ }
- /* calculate penalty for double bonds in valency angles */
- p_pen1 = thbp->p_pen1;
-
- exp_pen2ij = EXP( -p_pen2 * SQR( BOA_ij - 2.0 ) );
- exp_pen2jk = EXP( -p_pen2 * SQR( BOA_jk - 2.0 ) );
- exp_pen3 = EXP( -p_pen3 * workspace.Delta[j] );
- exp_pen4 = EXP( p_pen4 * workspace.Delta[j] );
- trm_pen34 = 1.0 + exp_pen3 + exp_pen4;
- f9_Dj = ( 2.0 + exp_pen3 ) / trm_pen34;
- Cf9j = (-p_pen3 * exp_pen3 * trm_pen34
- - (2.0 + exp_pen3) * ( -p_pen3 * exp_pen3
- + p_pen4 * exp_pen4 )) / SQR( trm_pen34 );
- /* very important: since each kernel generates all interactions,
- * need to prevent all energies becoming duplicates */
- if ( pk < pi )
- {
- e_pen = p_pen1 * f9_Dj * exp_pen2ij * exp_pen2jk;
- data_e_pen[j] += e_pen;
- }
+ /* calculate penalty for double bonds in valency angles */
+ p_pen1 = thbp->p_pen1;
+
+ exp_pen2ij = EXP( -p_pen2 * SQR( BOA_ij - 2.0 ) );
+ exp_pen2jk = EXP( -p_pen2 * SQR( BOA_jk - 2.0 ) );
+ exp_pen3 = EXP( -p_pen3 * workspace.Delta[j] );
+ exp_pen4 = EXP( p_pen4 * workspace.Delta[j] );
+ trm_pen34 = 1.0 + exp_pen3 + exp_pen4;
+ f9_Dj = ( 2.0 + exp_pen3 ) / trm_pen34;
+ Cf9j = (-p_pen3 * exp_pen3 * trm_pen34
+ - (2.0 + exp_pen3) * ( -p_pen3 * exp_pen3
+ + p_pen4 * exp_pen4 )) / SQR( trm_pen34 );
+
+ /* very important: since each kernel generates all interactions,
+ * need to prevent all energies becoming duplicates */
+ if ( pk < pi )
+ {
+ e_pen = p_pen1 * f9_Dj * exp_pen2ij * exp_pen2jk;
+#if !defined(CUDA_ACCUM_ENERGY_ATOMIC)
+ e_pen_g[j] += e_pen;
+#else
+ e_pen_l += e_pen;
+#endif
+ }
- CEpen1 = e_pen * Cf9j / f9_Dj;
- temp = -2.0 * p_pen2 * e_pen;
- CEpen2 = temp * (BOA_ij - 2.0);
- CEpen3 = temp * (BOA_jk - 2.0);
-
- /* calculate valency angle conjugation energy */
- p_coa1 = thbp->p_coa1;
-
- exp_coa2 = EXP( p_coa2 * workspace.Delta_boc[j] );
- e_coa = p_coa1
- * EXP( -p_coa4 * SQR(BOA_ij - 1.5) )
- * EXP( -p_coa4 * SQR(BOA_jk - 1.5) )
- * EXP( -p_coa3 * SQR(workspace.total_bond_order[i] - BOA_ij) )
- * EXP( -p_coa3 * SQR(workspace.total_bond_order[k] - BOA_jk) )
- / (1.0 + exp_coa2);
- /* similar to above comment regarding if statement */
- if ( pk < pi )
- {
- data_e_coa[j] += e_coa;
- }
+ CEpen1 = e_pen * Cf9j / f9_Dj;
+ temp = -2.0 * p_pen2 * e_pen;
+ CEpen2 = temp * (BOA_ij - 2.0);
+ CEpen3 = temp * (BOA_jk - 2.0);
+
+ /* calculate valency angle conjugation energy */
+ p_coa1 = thbp->p_coa1;
+
+ exp_coa2 = EXP( p_coa2 * workspace.Delta_boc[j] );
+ e_coa = p_coa1
+ * EXP( -p_coa4 * SQR(BOA_ij - 1.5) )
+ * EXP( -p_coa4 * SQR(BOA_jk - 1.5) )
+ * EXP( -p_coa3 * SQR(workspace.total_bond_order[i] - BOA_ij) )
+ * EXP( -p_coa3 * SQR(workspace.total_bond_order[k] - BOA_jk) )
+ / (1.0 + exp_coa2);
+ /* similar to above comment regarding if statement */
+ if ( pk < pi )
+ {
+#if !defined(CUDA_ACCUM_ENERGY_ATOMIC)
+ e_coa_g[j] += e_coa;
+#else
+ e_coa_l += e_coa;
+#endif
+ }
- CEcoa1 = -2.0 * p_coa4 * (BOA_ij - 1.5) * e_coa;
- CEcoa2 = -2.0 * p_coa4 * (BOA_jk - 1.5) * e_coa;
- CEcoa3 = -p_coa2 * exp_coa2 * e_coa / (1.0 + exp_coa2);
- CEcoa4 = -2.0 * p_coa3 * (workspace.total_bond_order[i] - BOA_ij) * e_coa;
- CEcoa5 = -2.0 * p_coa3 * (workspace.total_bond_order[k] - BOA_jk) * e_coa;
+ CEcoa1 = -2.0 * p_coa4 * (BOA_ij - 1.5) * e_coa;
+ CEcoa2 = -2.0 * p_coa4 * (BOA_jk - 1.5) * e_coa;
+ CEcoa3 = -p_coa2 * exp_coa2 * e_coa / (1.0 + exp_coa2);
+ CEcoa4 = -2.0 * p_coa3 * (workspace.total_bond_order[i] - BOA_ij) * e_coa;
+ CEcoa5 = -2.0 * p_coa3 * (workspace.total_bond_order[k] - BOA_jk) * e_coa;
- /* calculate force contributions */
- /* we must again check for pk < pi for entire forces part */
- if ( pk < pi )
- {
+ /* calculate force contributions */
+ /* we must again check for pk < pi for entire forces part */
+ if ( pk < pi )
+ {
#if !defined(CUDA_ACCUM_FORCE_ATOMIC)
- bo_ij->Cdbo += (CEval1 + CEpen2 + (CEcoa1 - CEcoa4));
- bo_jk->Cdbo += (CEval2 + CEpen3 + (CEcoa2 - CEcoa5));
- workspace.CdDelta[j] += ((CEval3 + CEval7) + CEpen1 + CEcoa3);
- pbond_ij->va_CdDelta += CEcoa4;
- pbond_jk->va_CdDelta += CEcoa5;
+ bo_ij->Cdbo += CEval1 + CEpen2 + (CEcoa1 - CEcoa4);
+ bo_jk->Cdbo += CEval2 + CEpen3 + (CEcoa2 - CEcoa5);
+ workspace.CdDelta[j] += (CEval3 + CEval7) + CEpen1 + CEcoa3;
+ pbond_ij->va_CdDelta += CEcoa4;
+ pbond_jk->va_CdDelta += CEcoa5;
#else
- atomicAdd( &bo_ij->Cdbo, CEval1 + CEpen2 + (CEcoa1 - CEcoa4) );
- atomicAdd( &bo_jk->Cdbo, CEval2 + CEpen3 + (CEcoa2 - CEcoa5) );
- atomicAdd( &workspace.CdDelta[j], (CEval3 + CEval7) + CEpen1 + CEcoa3 );
- atomicAdd( &workspace.CdDelta[i], CEcoa4 );
- atomicAdd( &workspace.CdDelta[k], CEcoa5 );
+ atomicAdd( &bo_ij->Cdbo, CEval1 + CEpen2 + (CEcoa1 - CEcoa4) );
+ atomicAdd( &bo_jk->Cdbo, CEval2 + CEpen3 + (CEcoa2 - CEcoa5) );
+ atomicAdd( &workspace.CdDelta[j], (CEval3 + CEval7) + CEpen1 + CEcoa3 );
+ atomicAdd( &workspace.CdDelta[i], CEcoa4 );
+ atomicAdd( &workspace.CdDelta[k], CEcoa5 );
#endif
- for ( t = start_j; t < end_j; ++t )
- {
- pbond_jt = &bond_list.bond_list[t];
- bo_jt = &pbond_jt->bo_data;
- temp_bo_jt = bo_jt->BO;
- temp = CUBE( temp_bo_jt );
- pBOjt7 = temp * temp * temp_bo_jt;
+ for ( t = start_j; t < end_j; ++t )
+ {
+ pbond_jt = &bond_list.bond_list[t];
+ bo_jt = &pbond_jt->bo_data;
+ temp_bo_jt = bo_jt->BO;
+ temp = CUBE( temp_bo_jt );
+ pBOjt7 = temp * temp * temp_bo_jt;
#if !defined(CUDA_ACCUM_FORCE_ATOMIC)
- bo_jt->Cdbo += (CEval6 * pBOjt7);
- bo_jt->Cdbopi += CEval5;
- bo_jt->Cdbopi2 += CEval5;
+ bo_jt->Cdbo += (CEval6 * pBOjt7);
+ bo_jt->Cdbopi += CEval5;
+ bo_jt->Cdbopi2 += CEval5;
#else
- atomicAdd( &bo_jt->Cdbo, CEval6 * pBOjt7 );
- atomicAdd( &bo_jt->Cdbopi, CEval5 );
- atomicAdd( &bo_jt->Cdbopi2, CEval5 );
+ atomicAdd( &bo_jt->Cdbo, CEval6 * pBOjt7 );
+ atomicAdd( &bo_jt->Cdbopi, CEval5 );
+ atomicAdd( &bo_jt->Cdbopi2, CEval5 );
#endif
- }
+ }
- if ( control->virial == 0 )
- {
+ if ( control->virial == 0 )
+ {
#if !defined(CUDA_ACCUM_FORCE_ATOMIC)
- rvec_ScaledAdd( pbond_ij->va_f, CEval8, p_ijk->dcos_di );
- rvec_ScaledAdd( workspace.f[j], CEval8, p_ijk->dcos_dj );
- rvec_ScaledAdd( pbond_jk->va_f, CEval8, p_ijk->dcos_dk );
+ rvec_ScaledAdd( pbond_ij->va_f, CEval8, p_ijk->dcos_di );
+ rvec_ScaledAdd( workspace.f[j], CEval8, p_ijk->dcos_dj );
+ rvec_ScaledAdd( pbond_jk->va_f, CEval8, p_ijk->dcos_dk );
#else
- atomic_rvecScaledAdd( workspace.f[i], CEval8, p_ijk->dcos_di );
- atomic_rvecScaledAdd( workspace.f[j], CEval8, p_ijk->dcos_dj );
- atomic_rvecScaledAdd( workspace.f[k], CEval8, p_ijk->dcos_dk );
+ atomic_rvecScaledAdd( workspace.f[i], CEval8, p_ijk->dcos_di );
+ atomic_rvecScaledAdd( workspace.f[j], CEval8, p_ijk->dcos_dj );
+ atomic_rvecScaledAdd( workspace.f[k], CEval8, p_ijk->dcos_dk );
#endif
- }
- else
- {
+ }
+ else
+ {
#if !defined(CUDA_ACCUM_FORCE_ATOMIC)
- /* terms not related to bond order derivatives are
- * added directly into forces and pressure vector/tensor */
- rvec_Scale( force, CEval8, p_ijk->dcos_di );
- rvec_Add( pbond_ij->va_f, force );
- rvec_iMultiply( ext_press, pbond_ij->rel_box, force );
- rvec_Add( my_ext_press[j], ext_press );
-
- rvec_ScaledAdd( workspace.f[j], CEval8, p_ijk->dcos_dj );
-
- rvec_Scale( force, CEval8, p_ijk->dcos_dk );
- rvec_Add( pbond_jk->va_f, force );
- rvec_iMultiply( ext_press, pbond_jk->rel_box, force );
- rvec_Add( my_ext_press[j], ext_press );
+ /* terms not related to bond order derivatives are
+ * added directly into forces and pressure vector/tensor */
+ rvec_Scale( force, CEval8, p_ijk->dcos_di );
+ rvec_Add( pbond_ij->va_f, force );
+ rvec_iMultiply( ext_press, pbond_ij->rel_box, force );
+#if !defined(CUDA_ACCUM_ENERGY_ATOMIC)
+ rvec_Add( ext_press_g[j], ext_press );
#else
- /* terms not related to bond order derivatives are
- * added directly into forces and pressure vector/tensor */
- rvec_Scale( force, CEval8, p_ijk->dcos_di );
- atomic_rvecAdd( workspace.f[i], force );
- rvec_iMultiply( ext_press, pbond_ij->rel_box, force );
- rvec_Add( my_ext_press[j], ext_press );
-
- rvec_ScaledAdd( workspace.f[j], CEval8, p_ijk->dcos_dj );
-
- rvec_Scale( force, CEval8, p_ijk->dcos_dk );
- atomic_rvecAdd( workspace.f[k], force );
- rvec_iMultiply( ext_press, pbond_jk->rel_box, force );
- rvec_Add( my_ext_press[j], ext_press );
-#endif
- }
- }
-
-#if defined(TEST_ENERGY)
- /*fprintf( out_control->eval, "%12.8f%12.8f%12.8f%12.8f\n",
- p_val3, p_val4, BOA_ij, BOA_jk );
- fprintf(out_control->eval, "%13.8f%13.8f%13.8f%13.8f%13.8f\n",
- workspace.Delta_e[j], workspace.vlpex[j],
- dSBO1, dSBO2, vlpadj );
- fprintf( out_control->eval, "%12.8f%12.8f%12.8f%12.8f\n",
- f7_ij, f7_jk, f8_Dj, expval12theta );
- fprintf( out_control->eval,
- "%12.8f%12.8f%12.8f%12.8f%12.8f%12.8f%12.8f%12.8f\n",
- CEval1, CEval2, CEval3, CEval4,
- CEval5, CEval6, CEval7, CEval8 );
-
- fprintf( out_control->eval,
- "%12.8f%12.8f%12.8f\n%12.8f%12.8f%12.8f\n%12.8f%12.8f%12.8f\n",
- p_ijk->dcos_di[0]/sin_theta, p_ijk->dcos_di[1]/sin_theta,
- p_ijk->dcos_di[2]/sin_theta,
- p_ijk->dcos_dj[0]/sin_theta, p_ijk->dcos_dj[1]/sin_theta,
- p_ijk->dcos_dj[2]/sin_theta,
- p_ijk->dcos_dk[0]/sin_theta, p_ijk->dcos_dk[1]/sin_theta,
- p_ijk->dcos_dk[2]/sin_theta);
-
- fprintf( out_control->eval,
- "%6d%6d%6d%15.8f%15.8f\n",
- system->my_atoms[i].orig_id,
- system->my_atoms[j].orig_id,
- system->my_atoms[k].orig_id,
- RAD2DEG(theta), e_ang );*/
-
- fprintf( out_control->eval,
- //"%6d%6d%6d%24.15e%24.15e%24.15e%24.15e%24.15e%24.15e\n",
- "%6d%6d%6d%12.4f%12.4f%12.4f%12.4f%12.4f%12.4f\n",
- system->my_atoms[i].orig_id,
- system->my_atoms[j].orig_id,
- system->my_atoms[k].orig_id,
- RAD2DEG(theta), theta_0, BOA_ij, BOA_jk,
- e_ang, data->my_en.e_ang );
-
- fprintf( out_control->epen,
- //"%6d%6d%6d%24.15e%24.15e%24.15e%24.15e%24.15e\n",
- "%6d%6d%6d%12.4f%12.4f%12.4f%12.4f%12.4f\n",
- system->my_atoms[i].orig_id,
- system->my_atoms[j].orig_id,
- system->my_atoms[k].orig_id,
- RAD2DEG(theta), BOA_ij, BOA_jk, e_pen,
- data->my_en.e_pen );
-
- fprintf( out_control->ecoa,
- //"%6d%6d%6d%24.15e%24.15e%24.15e%24.15e%24.15e\n",
- "%6d%6d%6d%12.4f%12.4f%12.4f%12.4f%12.4f\n",
- system->my_atoms[i].orig_id,
- system->my_atoms[j].orig_id,
- system->my_atoms[k].orig_id,
- RAD2DEG(theta), BOA_ij, BOA_jk,
- e_coa, data->my_en.e_coa );
+ rvec_Add( ext_press_g[j], ext_press_l );
#endif
-#if defined(TEST_FORCES)
- /* angle forces */
- Add_dBO( system, lists, j, pi, CEval1, workspace.f_ang );
- Add_dBO( system, lists, j, pk, CEval2, workspace.f_ang );
- Add_dDelta( system, lists, j,
- CEval3 + CEval7, workspace.f_ang );
+ rvec_ScaledAdd( workspace.f[j], CEval8, p_ijk->dcos_dj );
- for( t = start_j; t < end_j; ++t )
- {
- pbond_jt = &bond_list.bond_list[t];
- bo_jt = &pbond_jt->bo_data;
- temp_bo_jt = bo_jt->BO;
- temp = CUBE( temp_bo_jt );
- pBOjt7 = temp * temp * temp_bo_jt;
+ rvec_Scale( force, CEval8, p_ijk->dcos_dk );
+ rvec_Add( pbond_jk->va_f, force );
+ rvec_iMultiply( ext_press, pbond_jk->rel_box, force );
+#if !defined(CUDA_ACCUM_ENERGY_ATOMIC)
+ rvec_Add( ext_press_g[j], ext_press );
+#else
+ rvec_Add( ext_press_g[j], ext_press_l );
+#endif
+#else
+ /* terms not related to bond order derivatives are
+ * added directly into forces and pressure vector/tensor */
+ rvec_Scale( force, CEval8, p_ijk->dcos_di );
+ atomic_rvecAdd( workspace.f[i], force );
+ rvec_iMultiply( ext_press, pbond_ij->rel_box, force );
+#if !defined(CUDA_ACCUM_ENERGY_ATOMIC)
+ rvec_Add( ext_press_g[j], ext_press );
+#else
+ rvec_Add( ext_press_g[j], ext_press_l );
+#endif
- Add_dBO( system, lists, j, t, pBOjt7 * CEval6,
- workspace.f_ang );
- Add_dBOpinpi2( system, lists, j, t, CEval5, CEval5,
- workspace.f_ang, workspace.f_ang );
- }
+ rvec_ScaledAdd( workspace.f[j], CEval8, p_ijk->dcos_dj );
- rvec_ScaledAdd( workspace.f_ang[i], CEval8, p_ijk->dcos_di );
- rvec_ScaledAdd( workspace.f_ang[j], CEval8, p_ijk->dcos_dj );
- rvec_ScaledAdd( workspace.f_ang[k], CEval8, p_ijk->dcos_dk );
- /* end angle forces */
-
- /* penalty forces */
- Add_dDelta( system, lists, j, CEpen1, workspace.f_pen );
- Add_dBO( system, lists, j, pi, CEpen2, workspace.f_pen );
- Add_dBO( system, lists, j, pk, CEpen3, workspace.f_pen );
- /* end penalty forces */
-
- /* coalition forces */
- Add_dBO( system, lists, j, pi, CEcoa1 - CEcoa4,
- workspace.f_coa );
- Add_dBO( system, lists, j, pk, CEcoa2 - CEcoa5,
- workspace.f_coa );
- Add_dDelta( system, lists, j, CEcoa3, workspace.f_coa );
- Add_dDelta( system, lists, i, CEcoa4, workspace.f_coa );
- Add_dDelta( system, lists, k, CEcoa5, workspace.f_coa );
- /* end coalition forces */
+ rvec_Scale( force, CEval8, p_ijk->dcos_dk );
+ atomic_rvecAdd( workspace.f[k], force );
+ rvec_iMultiply( ext_press, pbond_jk->rel_box, force );
+#if !defined(CUDA_ACCUM_ENERGY_ATOMIC)
+ rvec_Add( ext_press_g[j], ext_press );
+#else
+ rvec_Add( ext_press_g[j], ext_press_l );
#endif
+#endif
+ }
}
}
}
@@ -546,6 +489,13 @@ CUDA_GLOBAL void Cuda_Valence_Angles_Part1( reax_atom *my_atoms,
Set_End_Index( pi, num_thb_intrs, &thb_list );
}
+
+#if defined(CUDA_ACCUM_ENERGY_ATOMIC)
+ atomicAdd( (double *) e_ang_g, (double) e_ang_l );
+ atomicAdd( (double *) e_coa_g, (double) e_coa_l );
+ atomicAdd( (double *) e_pen_g, (double) e_pen_l );
+ atomic_rvecAdd( *ext_press_g, ext_press_l );
+#endif
}
diff --git a/PG-PuReMD/src/cuda/cuda_valence_angles.h b/PG-PuReMD/src/cuda/cuda_valence_angles.h
index d91387d2..74df6b45 100644
--- a/PG-PuReMD/src/cuda/cuda_valence_angles.h
+++ b/PG-PuReMD/src/cuda/cuda_valence_angles.h
@@ -42,8 +42,8 @@ CUDA_GLOBAL void Cuda_Estimate_Valence_Angles( reax_atom *, control_params *,
/* calculates the theta angle between atom triplet i-j-k */
-CUDA_DEVICE static inline void Calculate_Theta( const rvec dvec_ji, real d_ji, rvec dvec_jk, real d_jk,
- real * const theta, real * const cos_theta )
+CUDA_DEVICE static inline void Calculate_Theta( const rvec dvec_ji, real d_ji,
+ const rvec dvec_jk, real d_jk, real * const theta, real * const cos_theta )
{
assert( d_ji > 0.0 );
assert( d_jk > 0.0 );
@@ -64,8 +64,9 @@ CUDA_DEVICE static inline void Calculate_Theta( const rvec dvec_ji, real d_ji, r
/* calculates the derivative of the cosine of the angle between atom triplet i-j-k */
-CUDA_DEVICE static inline void Calculate_dCos_Theta( const rvec dvec_ji, real d_ji, rvec dvec_jk, real d_jk,
- rvec * const dcos_theta_di, rvec * const dcos_theta_dj, rvec * const dcos_theta_dk )
+CUDA_DEVICE static inline void Calculate_dCos_Theta( const rvec dvec_ji,
+ real d_ji, const rvec dvec_jk, real d_jk, rvec * const dcos_theta_di,
+ rvec * const dcos_theta_dj, rvec * const dcos_theta_dk )
{
int t;
real sqr_d_ji, sqr_d_jk, inv_dists, inv_dists3, dot_dvecs, Cdot_inv3;
diff --git a/PG-PuReMD/src/reax_types.h b/PG-PuReMD/src/reax_types.h
index ef2fbaa1..127b2578 100644
--- a/PG-PuReMD/src/reax_types.h
+++ b/PG-PuReMD/src/reax_types.h
@@ -84,6 +84,8 @@
#endif
/* aggregate atomic forces using atomic operations */
#define CUDA_ACCUM_FORCE_ATOMIC
+/* aggregate atomic energies using atomic operations */
+#define CUDA_ACCUM_ENERGY_ATOMIC
/* disable assertions if NOT compiling with debug support --
* the definition (or lack thereof) controls how the assert macro is defined */
@@ -131,7 +133,7 @@
#if defined(USE_REF_FORTRAN_REAXFF_CONSTANTS)
/* transcendental constant pi */
- #define PI (3.14159265)
+// #define PI (3.14159265)
/* unit conversion from ??? to kcal / mol */
#define C_ELE (332.0638)
/* Boltzmann constant, AMU * A^2 / (ps^2 * K) */
diff --git a/test/library/qmmm_amber/forces_charges.txt b/test/library/qmmm_amber/forces_charges.txt
new file mode 100644
index 00000000..fe88a529
--- /dev/null
+++ b/test/library/qmmm_amber/forces_charges.txt
@@ -0,0 +1,777 @@
+Total Energy |Kinetic Energy |Potential Energy
+ -1374.311060684900440 0.000000000000000 -1374.311060684900440
+
+i |F_x |F_y |F_z |Q
+ 1 101.795785159104 -112.791218389056 91.729275100765 0.115792827421
+ 2 74.441831586489 -127.881951035570 175.497941779944 -0.458827596916
+ 3 -79.678635163780 275.299817782130 -6.125209056359 0.070840632741
+ 4 -88.632872232707 -102.053723908406 -198.791581562968 -0.047478739049
+ 5 15.609605985380 21.370352505907 -43.459224488185 -0.054830468036
+ 6 12.891298453587 19.844796781149 -28.298438011388 -0.062644558024
+ 7 -25.841707893576 17.405913183316 4.820262714472 0.067776819514
+ 8 4.330130660676 14.498948069526 -13.261491776472 0.031530359055
+ 9 -2.816499781569 2.454652467766 1.863859750108 0.055603650241
+ 10 -3.265212674584 -0.626171560718 2.197754344043 -0.007073276704
+ 11 1.569450698088 6.339172720895 -9.919553877391 0.054436086374
+ 12 -8.913931526567 -10.682924389337 11.008195804094 0.090306161444
+ 13 1.788942941122 1.415390304329 11.254019699132 0.056406471954
+ 14 -1.923466479132 -0.666972779086 -1.149368816080 0.088161629986
+ 15 -1.319583800108 -0.440845374930 1.296792972134 -0.834000000000
+ 16 0.675543028589 0.121765607414 -0.550015463024 0.417000000000
+ 17 0.738000809303 0.163411627921 -0.844842092094 0.417000000000
+ 18 -0.697834778580 -0.880335779378 1.071039059692 -0.834000000000
+ 19 0.238174324331 0.230471829704 -0.328026381719 0.417000000000
+ 20 0.551310194132 0.540821392078 -0.667365158250 0.417000000000
+ 21 -0.001507818490 -0.018421336054 0.008818580866 -0.834000000000
+ 22 -0.000659147026 0.021065901842 -0.009921912712 0.417000000000
+ 23 0.007025155658 0.046137962932 -0.020631530258 0.417000000000
+ 24 0.005937754480 -0.015939054184 0.041505491902 -0.834000000000
+ 25 -0.006573867985 0.026712714641 -0.079634537918 0.417000000000
+ 26 -0.000418165561 0.001307002132 -0.003873860586 0.417000000000
+ 27 -0.091751959010 -0.011419517522 0.081118676719 -0.834000000000
+ 28 0.022480288619 -0.000282084491 -0.020265744212 0.417000000000
+ 29 0.168808433594 0.025625054380 -0.158888645033 0.417000000000
+ 30 -0.067184660158 -0.157636335109 0.060341885228 -0.834000000000
+ 31 0.063222671761 0.113374708109 -0.053497578011 0.417000000000
+ 32 0.006268945127 0.014668132846 -0.005967337396 0.417000000000
+ 33 0.228532288950 -0.581601419919 0.557046037990 -0.834000000000
+ 34 -0.081472817682 0.373237714699 -0.316439120156 0.417000000000
+ 35 -0.191252315139 0.358866085543 -0.307855965855 0.417000000000
+ 36 -0.083936575704 -0.053289821120 0.101793790283 -0.834000000000
+ 37 0.021862599787 0.015376821532 -0.023183122487 0.417000000000
+ 38 0.055982808400 0.024453596424 -0.059101353887 0.417000000000
+ 39 -0.178700348066 -0.179072564979 0.017654436356 -0.834000000000
+ 40 0.011486196070 0.010529310012 -0.001449331462 0.417000000000
+ 41 0.050282798506 0.056898433706 -0.004128066251 0.417000000000
+ 42 -0.983620194147 1.089073960669 0.626806119470 -0.834000000000
+ 43 0.431204462226 -0.378513430781 -0.372943329812 0.417000000000
+ 44 0.324161047261 -0.587291851177 -0.128877449867 0.417000000000
+ 45 0.000010904533 0.000025770129 -0.000022669453 0.417000000000
+ 46 -0.089543653440 -0.083803195323 0.059312910380 -0.834000000000
+ 47 0.008196935416 0.006900305530 -0.004635010644 0.417000000000
+ 48 0.115829626443 0.107697222585 -0.069589733815 0.417000000000
+ 49 -0.038032016067 -0.124957045683 0.435439718413 -0.834000000000
+ 50 0.021796902281 0.059696335719 -0.152646774236 0.417000000000
+ 51 0.031096157214 0.033673891609 -0.176200474651 0.417000000000
+ 52 -0.049181087800 -0.006652299240 0.165750618389 -0.834000000000
+ 53 0.053361576970 -0.008036975414 -0.188197495142 0.417000000000
+ 54 0.007086233140 0.000976195966 -0.030253242968 0.417000000000
+ 55 -0.773136318983 -0.629643636841 0.300714515053 -0.834000000000
+ 56 0.232703940711 0.206514377685 -0.071984653984 0.417000000000
+ 57 0.529009597776 0.459468211802 -0.118830670859 0.417000000000
+ 58 0.008835013078 -0.023345721431 0.028022691106 -0.834000000000
+ 59 -0.022180174397 0.059538685884 -0.063201271754 0.417000000000
+ 60 -0.005564985551 0.016349491376 -0.023505775278 0.417000000000
+ 61 -0.350847270608 0.195762090476 0.372933630048 -0.834000000000
+ 62 0.118109297250 -0.056456599179 -0.131166361191 0.417000000000
+ 63 0.054389861958 -0.032285540050 -0.054700371420 0.417000000000
+ 64 -0.568577826634 -1.767122408120 0.290674957325 -0.834000000000
+ 65 0.247784509768 0.649481325260 -0.120975980763 0.417000000000
+ 66 0.440799875917 0.910808765507 -0.005510560417 0.417000000000
+ 67 -0.000605911543 0.000155562512 0.000601456366 -0.834000000000
+ 68 0.000842718036 -0.000225008695 -0.000892660483 0.417000000000
+ 69 -0.048805581315 -0.075283019773 0.137236584449 -0.834000000000
+ 70 0.026680897537 0.028691887580 -0.053861760301 0.417000000000
+ 71 0.015963431480 0.033256210873 -0.048190310078 0.417000000000
+ 72 -0.386255021722 -0.761273488618 2.002083042167 -0.834000000000
+ 73 0.089449756853 0.232476484061 -0.658889665506 0.417000000000
+ 74 0.294491690533 0.374488118211 -0.824861522546 0.417000000000
+ 75 -0.004997655577 0.001697958677 0.007505030369 -0.834000000000
+ 76 0.000997172504 -0.000172303919 -0.001630209383 0.417000000000
+ 77 0.017260726629 -0.009176133930 -0.030484004158 0.417000000000
+ 78 -0.442538774434 0.136697743502 0.662395997113 -0.834000000000
+ 79 0.377452577114 -0.079071081823 -0.622747428729 0.417000000000
+ 80 0.124739709749 -0.031528070347 -0.199206861638 0.417000000000
+ 81 0.000521175165 0.000075995231 -0.001086945367 0.417000000000
+ 82 0.000000528359 0.000000250498 -0.000008079996 0.417000000000
+ 83 -0.209058926347 0.201001723376 1.077553254957 -0.834000000000
+ 84 0.138434414703 -0.093389479519 -0.880339502157 0.417000000000
+ 85 0.068204991357 -0.171959614258 -0.544060960929 0.417000000000
+ 86 0.590829606900 -0.654396660280 1.542548034258 -0.834000000000
+ 87 -0.508847614472 0.370536533963 -0.890553344515 0.417000000000
+ 88 -0.251099737095 0.402776254498 -0.648752078774 0.417000000000
+ 89 0.000074492631 0.000015748039 -0.000052259325 0.417000000000
+ 90 0.000013086342 0.000002034524 -0.000008017244 0.417000000000
+ 91 -1.295983172838 0.135027441277 0.811813245094 -0.834000000000
+ 92 0.557789776589 -0.109781723422 -0.296883803551 0.417000000000
+ 93 0.622874195414 -0.155112363218 -0.488687913724 0.417000000000
+ 94 -1.370319587579 0.643161275807 1.962332591384 -0.834000000000
+ 95 0.552197409653 -0.352196800949 -1.182705185490 0.417000000000
+ 96 0.635618741398 -0.552771202648 -0.737991072254 0.417000000000
+ 97 -0.015959611649 -0.022608406429 0.000926530457 -0.834000000000
+ 98 0.019303638442 0.034108664896 -0.001251339771 0.417000000000
+ 99 0.000002352436 0.000003432362 -0.000000778642 0.417000000000
+ 100 -0.011779446505 -0.049929036761 0.047780071268 -0.834000000000
+ 101 0.025319077492 0.094800393251 -0.082454531431 0.417000000000
+ 102 0.001411839899 0.011066105621 -0.009227341752 0.417000000000
+ 103 -0.140062391878 -0.998735833279 0.702192318218 -0.834000000000
+ 104 0.094315496486 0.658000327114 -0.353335121296 0.417000000000
+ 105 0.165203300210 0.564054916210 -0.475555242114 0.417000000000
+ 106 0.061740983797 0.347156779272 -0.006832762966 -0.834000000000
+ 107 -0.003889576571 -0.134509516762 0.124565311304 0.417000000000
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diff --git a/test/library/qmmm_amber/fortran_stub/driver.F03 b/test/library/qmmm_amber/fortran_stub/driver.F03
index a61d3774..c097a977 100644
--- a/test/library/qmmm_amber/fortran_stub/driver.F03
+++ b/test/library/qmmm_amber/fortran_stub/driver.F03
@@ -69,7 +69,7 @@ contains
! Amber would set instead in real QM/MM simulation
read (line, '(30x,3f10.5,1x,a5,6x,f10.5)', end=40, err=40) &
mm_pos_q(4*nmm+1), mm_pos_q(4*nmm+2), mm_pos_q(4*nmm+3), &
- mm_types(nmm+1), mm_pos_q(4*nqm+4)
+ mm_types(nmm+1), mm_pos_q(4*nmm+4)
nmm = nmm + 1
endif
@@ -109,7 +109,7 @@ program driver
#define stderr 0
#endif
- integer, parameter :: max_sim_steps = 3
+ integer, parameter :: max_sim_steps = 0
character(len=1024), dimension(:), allocatable :: args
character(len=1024) :: filename
@@ -182,12 +182,20 @@ program driver
endif
end do
- do ix = 1, max_sim_steps
- call get_reaxff_puremd_forces( max_sim_steps, ix, sim_box_info, &
- num_qm_atoms, qm_pos, qm_types_map, qm_q, num_mm_atoms, &
- mm_pos_q, mm_types_map, e_total, qm_f, mm_f )
+ call get_reaxff_puremd_forces( max_sim_steps, 0, sim_box_info, &
+ num_qm_atoms, qm_pos, qm_types_map, qm_q, num_mm_atoms, &
+ mm_pos_q, mm_types_map, e_total, qm_f, mm_f )
- write (stdout, fmt=75) 'Sim. Step:', ix, 'Total energy:', e_total
+ write (stdout, fmt=75) 'Total energy:', e_total
+ write (stdout, *)
+ write (stdout, fmt=79) 'i', 'F_x', 'F_y', 'F_z', 'Q'
+ do ix = 1, num_qm_atoms
+ write (stdout, fmt=80) ix, qm_f(3 * (ix - 1) + 1), &
+ qm_f(3 * (ix - 1) + 2), qm_f(3 * (ix - 1) + 3), qm_q(ix)
+ end do
+ do ix = 1, num_mm_atoms
+ write (stdout, fmt=80) ix + num_qm_atoms, mm_f(3 * (ix - 1) + 1), &
+ mm_f(3 * (ix - 1) + 2), mm_f(3 * (ix - 1) + 3), mm_pos_q(4 * (ix - 1) + 3)
end do
deallocate(args)
@@ -201,5 +209,7 @@ program driver
deallocate(mm_pos_q)
deallocate(mm_f)
- 75 format (A10, 1X, I3, 1X, A13, 1X, ES24.15)
+ 75 format (A13, 1X, F24.15)
+ 79 format (A6, '|', A24, '|', A24, '|', A24, '|', A24)
+ 80 format (I6, 1X, F24.15, 1X, F24.15, 1X, F24.15, 1X, F24.15)
end program driver
diff --git a/test/library/qmmm_amber/fortran_stub/forces_charges.txt b/test/library/qmmm_amber/fortran_stub/forces_charges.txt
new file mode 100644
index 00000000..bf0d18f9
--- /dev/null
+++ b/test/library/qmmm_amber/fortran_stub/forces_charges.txt
@@ -0,0 +1,776 @@
+Total energy: -1374.311060684903623
+
+ i| F_x| F_y| F_z| Q
+ 1 101.795785159103403 -112.791218389056198 91.729275100765562 0.115792827420965
+ 2 74.441831586487424 -127.881951035566928 175.497941779944568 -0.458827596916358
+ 3 -79.678635163780541 275.299817782127434 -6.125209056360313 0.070840632740617
+ 4 -88.632872232706347 -102.053723908404720 -198.791581562965433 -0.047478739049226
+ 5 15.609605985380071 21.370352505906997 -43.459224488184844 -0.054830468036059
+ 6 12.891298453586931 19.844796781148922 -28.298438011388235 -0.062644558024110
+ 7 -25.841707893575201 17.405913183314592 4.820262714472239 0.067776819514187
+ 8 4.330130660675830 14.498948069525134 -13.261491776471846 0.031530359055013
+ 9 -2.816499781569538 2.454652467765156 1.863859750106969 0.055603650241363
+ 10 -3.265212674584364 -0.626171560718239 2.197754344042865 -0.007073276703923
+ 11 1.569450698087940 6.339172720894704 -9.919553877391289 0.054436086373693
+ 12 -8.913931526567165 -10.682924389337582 11.008195804094409 0.090306161443704
+ 13 1.788942941121586 1.415390304328931 11.254019699132716 0.056406471953649
+ 14 -1.923466479131818 -0.666972779086753 -1.149368816080454 0.088161629986456
+ 15 -1.319583800107266 -0.440845374929399 1.296792972133692 5.292260000000000
+ 16 0.675543028588913 0.121765607413734 -0.550015463023671 4.905660000000000
+ 17 0.738000809302813 0.163411627921033 -0.844842092094151 5.351760000000000
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+ 764 0.000000000000000 0.000000000000000 0.000000000000000 -11.042389999999999
+ 765 0.000000000000000 0.000000000000000 0.000000000000000 -11.164500000000000
+ 766 0.000000000000000 0.000000000000000 0.000000000000000 -11.139790000000000
+ 767 0.000000000000000 0.000000000000000 0.000000000000000 -11.141360000000001
+ 768 0.000000000000000 0.000000000000000 0.000000000000000 -10.162400000000000
+ 769 0.000000000000000 0.000000000000000 0.000000000000000 -9.436180000000000
+ 770 0.000000000000000 0.000000000000000 0.000000000000000 -9.761530000000000
+ 771 0.000000000000000 0.000000000000000 0.000000000000000 -10.909630000000000
+ 772 0.000000000000000 0.000000000000000 0.000000000000000 -10.890829999999999
+ 773 0.000000000000000 0.000000000000000 0.000000000000000 -8.075450000000000
diff --git a/test/library/qmmm_amber/fortran_stub/reaxff_puremd.F03 b/test/library/qmmm_amber/fortran_stub/reaxff_puremd.F03
index dfa29adb..7920792d 100644
--- a/test/library/qmmm_amber/fortran_stub/reaxff_puremd.F03
+++ b/test/library/qmmm_amber/fortran_stub/reaxff_puremd.F03
@@ -213,7 +213,7 @@ contains
! 0.001 threshold for valence angle interactions
keyword = "thb_cutoff" // char(0)
- values = "0.001" // char(0)
+ values = "0.005" // char(0)
ret = set_control_parameter( handle, c_loc(keyword), c_loc(values) )
if ( ret /= 0_c_int ) stop "ERROR: set_control_parameter"
diff --git a/test/library/qmmm_amber/fortran_stub/run_sim.bash b/test/library/qmmm_amber/fortran_stub/run_sim.bash
index 6e7d96eb..6a21ea2e 100644
--- a/test/library/qmmm_amber/fortran_stub/run_sim.bash
+++ b/test/library/qmmm_amber/fortran_stub/run_sim.bash
@@ -7,5 +7,6 @@ PROG="./driver"
BGF_FILE="../AVE/fort.3"
NUM_QM_ATOMS="14"
NUM_MM_ATOMS="759"
+LOG_FILE="forces_charges.txt"
-"${PROG}" "${BGF_FILE}" "${NUM_QM_ATOMS}" "${NUM_MM_ATOMS}"
+"${PROG}" "${BGF_FILE}" "${NUM_QM_ATOMS}" "${NUM_MM_ATOMS}" > "${LOG_FILE}"
diff --git a/test/library/qmmm_amber/tester_AVE.py b/test/library/qmmm_amber/tester_AVE.py
index f76f6e6f..62ef0978 100644
--- a/test/library/qmmm_amber/tester_AVE.py
+++ b/test/library/qmmm_amber/tester_AVE.py
@@ -363,7 +363,7 @@ if __name__ == '__main__':
setup_qmmm = lib.setup_qmmm
setup_qmmm.argtypes = [c_int, POINTER(c_int), POINTER(c_double),
c_int, POINTER(c_int), POINTER(c_double), POINTER(c_double),
- POINTER(c_double), c_char_p, c_char_p]
+ c_char_p, c_char_p]
setup_qmmm.restype = c_void_p
simulate = lib.simulate
@@ -436,11 +436,16 @@ if __name__ == '__main__':
qm_types = (c_int * num_qm_atoms)(*types[0:num_qm_atoms])
qm_p = (c_double * (3 * num_qm_atoms))(*p[0:(3 * num_qm_atoms)])
mm_types = (c_int * num_mm_atoms)(*types[num_qm_atoms:])
- mm_p = (c_double * (3 * num_mm_atoms))(*p[(3 * num_qm_atoms):])
- mm_q = (c_double * num_mm_atoms)(*q[num_qm_atoms:])
+ p_q = []
+ for i in range(num_mm_atoms):
+ p_q.append(p[3 * (num_qm_atoms + i)])
+ p_q.append(p[3 * (num_qm_atoms + i) + 1])
+ p_q.append(p[3 * (num_qm_atoms + i) + 2])
+ p_q.append(q[num_qm_atoms + i])
+ mm_p_q = (c_double * (4 * num_mm_atoms))(*p_q)
handle = setup_qmmm(c_int(num_qm_atoms), qm_types, qm_p,
- c_int(num_mm_atoms), mm_types, mm_p, mm_q, sim_box_info,
+ c_int(num_mm_atoms), mm_types, mm_p_q, sim_box_info,
b"AVE/ffield", None)
d = {
--
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