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reaxc_init_md.cpp
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/*----------------------------------------------------------------------
PuReMD - Purdue ReaxFF Molecular Dynamics Program
Copyright (2010) Purdue University
Hasan Metin Aktulga, hmaktulga@lbl.gov
Joseph Fogarty, jcfogart@mail.usf.edu
Sagar Pandit, pandit@usf.edu
Ananth Y Grama, ayg@cs.purdue.edu
Please cite the related publication:
H. M. Aktulga, J. C. Fogarty, S. A. Pandit, A. Y. Grama,
"Parallel Reactive Molecular Dynamics: Numerical Methods and
Algorithmic Techniques", Parallel Computing, in press.
This program is free software; you can redistribute it and/or
modify it under the terms of the GNU General Public License as
published by the Free Software Foundation; either version 2 of
the License, or (at your option) any later version.
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
See the GNU General Public License for more details:
<http://www.gnu.org/licenses/>.
----------------------------------------------------------------------*/
#include "pair_reax_c.h"
#if defined(PURE_REAX)
#include "init_md.h"
#include "allocate.h"
#include "box.h"
#include "comm_tools.h"
#include "forces.h"
#include "grid.h"
#include "integrate.h"
#include "io_tools.h"
#include "list.h"
#include "lookup.h"
#include "neighbors.h"
#include "random.h"
#include "reset_tools.h"
#include "system_props.h"
#include "tool_box.h"
#include "vector.h"
#elif defined(LAMMPS_REAX)
#include "reaxc_init_md.h"
#include "reaxc_allocate.h"
#include "reaxc_forces.h"
#include "reaxc_io_tools.h"
#include "reaxc_list.h"
#include "reaxc_lookup.h"
#include "reaxc_reset_tools.h"
#include "reaxc_system_props.h"
#include "reaxc_tool_box.h"
#include "reaxc_vector.h"
#endif
#if defined(PURE_REAX)
/************************ initialize system ************************/
int Reposition_Atoms( reax_system *system, control_params *control,
simulation_data *data, mpi_datatypes *mpi_data,
char *msg )
{
int i;
rvec dx;
/* reposition atoms */
if( control->reposition_atoms == 0 ) { //fit atoms to periodic box
rvec_MakeZero( dx );
}
else if( control->reposition_atoms == 1 ) { //put center of mass to center
rvec_Scale( dx, 0.5, system->big_box.box_norms );
rvec_ScaledAdd( dx, -1., data->xcm );
}
else if( control->reposition_atoms == 2 ) { //put center of mass to origin
rvec_Scale( dx, -1., data->xcm );
}
else {
strcpy( msg, "reposition_atoms: invalid option" );
return FAILURE;
}
for( i = 0; i < system->n; ++i )
// Inc_on_T3_Gen( system->my_atoms[i].x, dx, &(system->big_box) );
rvec_Add( system->my_atoms[i].x, dx );
return SUCCESS;
}
void Generate_Initial_Velocities( reax_system *system, real T )
{
int i;
real m, scale, norm;
if( T <= 0.1 ) {
for( i = 0; i < system->n; i++ )
rvec_MakeZero( system->my_atoms[i].v );
}
else {
Randomize();
for( i = 0; i < system->n; i++ ) {
rvec_Random( system->my_atoms[i].v );
norm = rvec_Norm_Sqr( system->my_atoms[i].v );
m = system->reax_param.sbp[ system->my_atoms[i].type ].mass;
scale = sqrt( m * norm / (3.0 * K_B * T) );
rvec_Scale( system->my_atoms[i].v, 1./scale, system->my_atoms[i].v );
// fprintf( stderr, "v = %f %f %f\n",
// system->my_atoms[i].v[0],
// system->my_atoms[i].v[1],
// system->my_atoms[i].v[2] );
// fprintf( stderr, "scale = %f\n", scale );
// fprintf( stderr, "v = %f %f %f\n",
// system->my_atoms[i].v[0],
// system->my_atoms[i].v[1],
// system->my_atoms[i].v[2] );
}
}
}
int Init_System( reax_system *system, control_params *control,
simulation_data *data, storage *workspace,
mpi_datatypes *mpi_data, char *msg )
{
int i;
reax_atom *atom;
int nrecv[MAX_NBRS];
Setup_New_Grid( system, control, mpi_data->world );
#if defined(DEBUG_FOCUS)
fprintf( stderr, "p%d GRID:\n", system->my_rank );
Print_Grid( &(system->my_grid), stderr );
#endif
Bin_My_Atoms( system, &(workspace->realloc) );
Reorder_My_Atoms( system, workspace );
/* estimate N and total capacity */
for( i = 0; i < MAX_NBRS; ++i ) nrecv[i] = 0;
system->max_recved = 0;
system->N = SendRecv( system, mpi_data, mpi_data->boundary_atom_type, nrecv,
Estimate_Boundary_Atoms, Unpack_Estimate_Message, 1 );
system->total_cap = MAX( (int)(system->N * SAFE_ZONE), MIN_CAP );
Bin_Boundary_Atoms( system );
/* estimate numH and Hcap */
system->numH = 0;
if( control->hbond_cut > 0 )
for( i = 0; i < system->n; ++i ) {
atom = &(system->my_atoms[i]);
if( system->reax_param.sbp[ atom->type ].p_hbond == 1 )
atom->Hindex = system->numH++;
else atom->Hindex = -1;
}
system->Hcap = MAX( system->numH * SAFER_ZONE, MIN_CAP );
//Allocate_System( system, system->local_cap, system->total_cap, msg );
#if defined(DEBUG_FOCUS)
fprintf( stderr, "p%d: n=%d local_cap=%d\n",
system->my_rank, system->n, system->local_cap );
fprintf( stderr, "p%d: N=%d total_cap=%d\n",
system->my_rank, system->N, system->total_cap );
fprintf( stderr, "p%d: numH=%d H_cap=%d\n",
system->my_rank, system->numH, system->Hcap );
#endif
// if( Reposition_Atoms( system, control, data, mpi_data, msg ) == FAILURE )
// return FAILURE;
/* initialize velocities so that desired init T can be attained */
if( !control->restart || (control->restart && control->random_vel) )
Generate_Initial_Velocities( system, control->T_init );
return SUCCESS;
}
/************************ initialize simulation data ************************/
int Init_Simulation_Data( reax_system *system, control_params *control,
simulation_data *data, mpi_datatypes *mpi_data,
char *msg )
{
Reset_Simulation_Data( data, control->virial );
if( !control->restart )
data->step = data->prev_steps = 0;
Compute_Total_Mass( system, data, mpi_data->comm_mesh3D );
Compute_Center_of_Mass( system, data, mpi_data, mpi_data->comm_mesh3D );
Compute_Kinetic_Energy( system, data, mpi_data->comm_mesh3D );
switch( control->ensemble ){
case NVE:
data->N_f = 3 * system->bigN;
Evolve = Velocity_Verlet_NVE;
break;
case bNVT:
data->N_f = 3 * system->bigN + 1;
Evolve = Velocity_Verlet_Berendsen_NVT;
break;
case nhNVT:
fprintf( stderr, "WARNING: Nose-Hoover NVT is still under testing.\n" );
//return FAILURE;
data->N_f = 3 * system->bigN + 1;
Evolve = Velocity_Verlet_Nose_Hoover_NVT_Klein;
if( !control->restart || (control->restart && control->random_vel) ) {
data->therm.G_xi = control->Tau_T *
(2.0 * data->sys_en.e_kin - data->N_f * K_B * control->T );
data->therm.v_xi = data->therm.G_xi * control->dt;
data->therm.v_xi_old = 0;
data->therm.xi = 0;
}
break;
case sNPT: /* Semi-Isotropic NPT */
data->N_f = 3 * system->bigN + 4;
Evolve = Velocity_Verlet_Berendsen_NPT;
if( !control->restart )
Reset_Pressures( data );
break;
case iNPT: /* Isotropic NPT */
data->N_f = 3 * system->bigN + 2;
Evolve = Velocity_Verlet_Berendsen_NPT;
if( !control->restart )
Reset_Pressures( data );
break;
case NPT: /* Anisotropic NPT */
strcpy( msg, "init_simulation_data: option not yet implemented" );
return FAILURE;
data->N_f = 3 * system->bigN + 9;
Evolve = Velocity_Verlet_Berendsen_NPT;
/*if( !control->restart ) {
data->therm.G_xi = control->Tau_T *
(2.0 * data->my_en.e_Kin - data->N_f * K_B * control->T );
data->therm.v_xi = data->therm.G_xi * control->dt;
data->iso_bar.eps = 0.33333 * log(system->box.volume);
data->inv_W = 1.0 /
( data->N_f * K_B * control->T * SQR(control->Tau_P) );
Compute_Pressure( system, control, data, out_control );
}*/
break;
default:
strcpy( msg, "init_simulation_data: ensemble not recognized" );
return FAILURE;
}
/* initialize the timer(s) */
MPI_Barrier( mpi_data->world ); // wait for everyone to come here
if( system->my_rank == MASTER_NODE ) {
data->timing.start = Get_Time( );
#if defined(LOG_PERFORMANCE)
Reset_Timing( &data->timing );
#endif
}
#if defined(DEBUG)
fprintf( stderr, "data->N_f: %8.3f\n", data->N_f );
#endif
return SUCCESS;
}
#elif defined(LAMMPS_REAX)
int Init_System( reax_system *system, control_params *control, char *msg )
{
int i;
reax_atom *atom;
int mincap = system->mincap;
double safezone = system->safezone;
double saferzone = system->saferzone;
// determine the local and total capacity
system->local_cap = MAX( (int)(system->n * safezone), mincap);
system->total_cap = MAX( (int)(system->N * safezone), mincap);
/* estimate numH and Hcap */
system->numH = 0;
if( control->hbond_cut > 0 )
for( i = 0; i < system->n; ++i ) {
atom = &(system->my_atoms[i]);
if( system->reax_param.sbp[ atom->type ].p_hbond == 1 )
atom->Hindex = system->numH++;
else atom->Hindex = -1;
}
system->Hcap = (int)(MAX( system->numH * saferzone, mincap ));
#if defined(DEBUG_FOCUS)
fprintf( stderr, "p%d: n=%d local_cap=%d\n",
system->my_rank, system->n, system->local_cap );
fprintf( stderr, "p%d: N=%d total_cap=%d\n",
system->my_rank, system->N, system->total_cap );
fprintf( stderr, "p%d: numH=%d H_cap=%d\n",
system->my_rank, system->numH, system->Hcap );
#endif
return SUCCESS;
}
int Init_Simulation_Data( reax_system *system, control_params *control,
simulation_data *data, char *msg )
{
Reset_Simulation_Data( data, control->virial );
/* initialize the timer(s) */
if( system->my_rank == MASTER_NODE ) {
data->timing.start = Get_Time( );
#if defined(LOG_PERFORMANCE)
Reset_Timing( &data->timing );
#endif
}
//if( !control->restart )
data->step = data->prev_steps = 0;
return SUCCESS;
}
#endif
/************************ initialize workspace ************************/
/* Initialize Taper params */
void Init_Taper( control_params *control, storage *workspace, MPI_Comm comm )
{
real d1, d7;
real swa, swa2, swa3;
real swb, swb2, swb3;
swa = control->nonb_low;
swb = control->nonb_cut;
if( fabs( swa ) > 0.01 )
fprintf( stderr, "Warning: non-zero lower Taper-radius cutoff\n" );
if( swb < 0 ) {
fprintf( stderr, "Negative upper Taper-radius cutoff\n" );
MPI_Abort( comm, INVALID_INPUT );
}
else if( swb < 5 )
fprintf( stderr, "Warning: very low Taper-radius cutoff: %f\n", swb );
d1 = swb - swa;
d7 = pow( d1, 7.0 );
swa2 = SQR( swa );
swa3 = CUBE( swa );
swb2 = SQR( swb );
swb3 = CUBE( swb );
workspace->Tap[7] = 20.0 / d7;
workspace->Tap[6] = -70.0 * (swa + swb) / d7;
workspace->Tap[5] = 84.0 * (swa2 + 3.0*swa*swb + swb2) / d7;
workspace->Tap[4] = -35.0 * (swa3 + 9.0*swa2*swb + 9.0*swa*swb2 + swb3 ) / d7;
workspace->Tap[3] = 140.0 * (swa3*swb + 3.0*swa2*swb2 + swa*swb3 ) / d7;
workspace->Tap[2] =-210.0 * (swa3*swb2 + swa2*swb3) / d7;
workspace->Tap[1] = 140.0 * swa3 * swb3 / d7;
workspace->Tap[0] = (-35.0*swa3*swb2*swb2 + 21.0*swa2*swb3*swb2 +
7.0*swa*swb3*swb3 + swb3*swb3*swb ) / d7;
}
int Init_Workspace( reax_system *system, control_params *control,
storage *workspace, MPI_Comm comm, char *msg )
{
int ret;
ret = Allocate_Workspace( system, control, workspace,
system->local_cap, system->total_cap, comm, msg );
if( ret != SUCCESS )
return ret;
memset( &(workspace->realloc), 0, sizeof(reallocate_data) );
Reset_Workspace( system, workspace );
/* Initialize the Taper function */
Init_Taper( control, workspace, comm );
return SUCCESS;
}
/************** setup communication data structures **************/
int Init_MPI_Datatypes( reax_system *system, storage *workspace,
mpi_datatypes *mpi_data, MPI_Comm comm, char *msg )
{
#if defined(PURE_REAX)
int i, block[11];
MPI_Aint base, disp[11];
MPI_Datatype type[11];
mpi_atom sample;
boundary_atom b_sample;
restart_atom r_sample;
rvec rvec_sample;
rvec2 rvec2_sample;
#endif
/* setup the world */
mpi_data->world = comm;
MPI_Comm_size( comm, &(system->wsize) );
#if defined(PURE_REAX)
/* init mpi buffers */
mpi_data->in1_buffer = NULL;
mpi_data->in2_buffer = NULL;
/* mpi_atom - [orig_id, imprt_id, type, num_bonds, num_hbonds, name,
x, v, f_old, s, t] */
block[0] = block[1] = block[2] = block[3] = block[4] = 1;
block[5] = 8;
block[6] = block[7] = block[8] = 3;
block[9] = block[10] = 4;
MPI_Address( &(sample.orig_id), disp + 0 );
MPI_Address( &(sample.imprt_id), disp + 1 );
MPI_Address( &(sample.type), disp + 2 );
MPI_Address( &(sample.num_bonds), disp + 3 );
MPI_Address( &(sample.num_hbonds), disp + 4 );
MPI_Address( &(sample.name), disp + 5 );
MPI_Address( &(sample.x[0]), disp + 6 );
MPI_Address( &(sample.v[0]), disp + 7 );
MPI_Address( &(sample.f_old[0]), disp + 8 );
MPI_Address( &(sample.s[0]), disp + 9 );
MPI_Address( &(sample.t[0]), disp + 10 );
base = (MPI_Aint)(&(sample));
for( i = 0; i < 11; ++i ) disp[i] -= base;
type[0] = type[1] = type[2] = type[3] = type[4] = MPI_INT;
type[5] = MPI_CHAR;
type[6] = type[7] = type[8] = type[9] = type[10] = MPI_DOUBLE;
MPI_Type_struct( 11, block, disp, type, &(mpi_data->mpi_atom_type) );
MPI_Type_commit( &(mpi_data->mpi_atom_type) );
/* boundary_atom - [orig_id, imprt_id, type, num_bonds, num_hbonds, x] */
block[0] = block[1] = block[2] = block[3] = block[4] = 1;
block[5] = 3;
MPI_Address( &(b_sample.orig_id), disp + 0 );
MPI_Address( &(b_sample.imprt_id), disp + 1 );
MPI_Address( &(b_sample.type), disp + 2 );
MPI_Address( &(b_sample.num_bonds), disp + 3 );
MPI_Address( &(b_sample.num_hbonds), disp + 4 );
MPI_Address( &(b_sample.x[0]), disp + 5 );
base = (MPI_Aint)(&(b_sample));
for( i = 0; i < 6; ++i ) disp[i] -= base;
type[0] = type[1] = type[2] = type[3] = type[4] = MPI_INT;
type[5] = MPI_DOUBLE;
MPI_Type_struct( 6, block, disp, type, &(mpi_data->boundary_atom_type) );
MPI_Type_commit( &(mpi_data->boundary_atom_type) );
/* mpi_rvec */
block[0] = 3;
MPI_Address( &(rvec_sample[0]), disp + 0 );
base = disp[0];
for( i = 0; i < 1; ++i ) disp[i] -= base;
type[0] = MPI_DOUBLE;
MPI_Type_struct( 1, block, disp, type, &(mpi_data->mpi_rvec) );
MPI_Type_commit( &(mpi_data->mpi_rvec) );
/* mpi_rvec2 */
block[0] = 2;
MPI_Address( &(rvec2_sample[0]), disp + 0 );
base = disp[0];
for( i = 0; i < 1; ++i ) disp[i] -= base;
type[0] = MPI_DOUBLE;
MPI_Type_struct( 1, block, disp, type, &(mpi_data->mpi_rvec2) );
MPI_Type_commit( &(mpi_data->mpi_rvec2) );
/* restart_atom - [orig_id, type, name[8], x, v] */
block[0] = block[1] = 1 ;
block[2] = 8;
block[3] = block[4] = 3;
MPI_Address( &(r_sample.orig_id), disp + 0 );
MPI_Address( &(r_sample.type), disp + 1 );
MPI_Address( &(r_sample.name), disp + 2 );
MPI_Address( &(r_sample.x[0]), disp + 3 );
MPI_Address( &(r_sample.v[0]), disp + 4 );
base = (MPI_Aint)(&(r_sample));
for( i = 0; i < 5; ++i ) disp[i] -= base;
type[0] = type[1] = MPI_INT;
type[2] = MPI_CHAR;
type[3] = type[4] = MPI_DOUBLE;
MPI_Type_struct( 5, block, disp, type, &(mpi_data->restart_atom_type) );
MPI_Type_commit( &(mpi_data->restart_atom_type) );
#endif
return SUCCESS;
}
/********************** allocate lists *************************/
#if defined(PURE_REAX)
int Init_Lists( reax_system *system, control_params *control,
simulation_data *data, storage *workspace, reax_list **lists,
mpi_datatypes *mpi_data, char *msg )
{
int i, num_nbrs;
int total_hbonds, total_bonds, bond_cap, num_3body, cap_3body, Htop;
int *hb_top, *bond_top;
MPI_Comm comm;
comm = mpi_data->world;
//for( i = 0; i < MAX_NBRS; ++i ) nrecv[i] = system->my_nbrs[i].est_recv;
//system->N = SendRecv( system, mpi_data, mpi_data->boundary_atom_type, nrecv,
// Sort_Boundary_Atoms, Unpack_Exchange_Message, 1 );
num_nbrs = Estimate_NumNeighbors( system, lists );
if(!Make_List( system->total_cap, num_nbrs, TYP_FAR_NEIGHBOR,
*lists+FAR_NBRS, comm )){
fprintf(stderr, "Problem in initializing far nbrs list. Terminating!\n");
MPI_Abort( comm, INSUFFICIENT_MEMORY );
}
#if defined(DEBUG_FOCUS)
fprintf( stderr, "p%d: allocated far_nbrs: num_far=%d, space=%dMB\n",
system->my_rank, num_nbrs,
(int)(num_nbrs*sizeof(far_neighbor_data)/(1024*1024)) );
#endif
Generate_Neighbor_Lists( system, data, workspace, lists );
bond_top = (int*) calloc( system->total_cap, sizeof(int) );
hb_top = (int*) calloc( system->local_cap, sizeof(int) );
Estimate_Storages( system, control, lists,
&Htop, hb_top, bond_top, &num_3body, comm );
Allocate_Matrix( &(workspace->H), system->local_cap, Htop, comm );
workspace->L = NULL;
workspace->U = NULL;
#if defined(DEBUG_FOCUS)
fprintf( stderr, "p%d: allocated H matrix: Htop=%d, space=%dMB\n",
system->my_rank, Htop,
(int)(Htop * sizeof(sparse_matrix_entry) / (1024*1024)) );
#endif
if( control->hbond_cut > 0 ) {
/* init H indexes */
total_hbonds = 0;
for( i = 0; i < system->n; ++i ) {
system->my_atoms[i].num_hbonds = hb_top[i];
total_hbonds += hb_top[i];
}
total_hbonds = MAX( total_hbonds*SAFER_ZONE, MIN_CAP*MIN_HBONDS );
if( !Make_List( system->Hcap, total_hbonds, TYP_HBOND,
*lists+HBONDS, comm ) ) {
fprintf( stderr, "not enough space for hbonds list. terminating!\n" );
MPI_Abort( comm, INSUFFICIENT_MEMORY );
}
#if defined(DEBUG_FOCUS)
fprintf( stderr, "p%d: allocated hbonds: total_hbonds=%d, space=%dMB\n",
system->my_rank, total_hbonds,
(int)(total_hbonds*sizeof(hbond_data)/(1024*1024)) );
#endif
}
/* bonds list */
//Allocate_Bond_List( system->N, bond_top, (*lists)+BONDS );
//num_bonds = bond_top[system->N-1];
total_bonds = 0;
for( i = 0; i < system->N; ++i ) {
system->my_atoms[i].num_bonds = bond_top[i];
total_bonds += bond_top[i];
}
bond_cap = MAX( total_bonds*SAFE_ZONE, MIN_CAP*MIN_BONDS );
if( !Make_List( system->total_cap, bond_cap, TYP_BOND,
*lists+BONDS, comm ) ) {
fprintf( stderr, "not enough space for bonds list. terminating!\n" );
MPI_Abort( comm, INSUFFICIENT_MEMORY );
}
#if defined(DEBUG_FOCUS)
fprintf( stderr, "p%d: allocated bonds: total_bonds=%d, space=%dMB\n",
system->my_rank, bond_cap,
(int)(bond_cap*sizeof(bond_data)/(1024*1024)) );
#endif
/* 3bodies list */
cap_3body = MAX( num_3body*SAFE_ZONE, MIN_3BODIES );
if( !Make_List( bond_cap, cap_3body, TYP_THREE_BODY,
*lists+THREE_BODIES, comm ) ){
fprintf( stderr, "Problem in initializing angles list. Terminating!\n" );
MPI_Abort( comm, INSUFFICIENT_MEMORY );
}
#if defined(DEBUG_FOCUS)
fprintf( stderr, "p%d: allocated 3-body list: num_3body=%d, space=%dMB\n",
system->my_rank, cap_3body,
(int)(cap_3body*sizeof(three_body_interaction_data)/(1024*1024)) );
#endif
#if defined(TEST_FORCES)
if( !Make_List( system->total_cap, bond_cap*8, TYP_DDELTA,
*lists+DDELTAS, comm ) ) {
fprintf( stderr, "Problem in initializing dDelta list. Terminating!\n" );
MPI_Abort( comm, INSUFFICIENT_MEMORY );
}
fprintf( stderr, "p%d: allocated dDelta list: num_ddelta=%d space=%ldMB\n",
system->my_rank, bond_cap*30,
bond_cap*8*sizeof(dDelta_data)/(1024*1024) );
if( !Make_List( bond_cap, bond_cap*50, TYP_DBO, *lists+DBOS, comm ) ) {
fprintf( stderr, "Problem in initializing dBO list. Terminating!\n" );
MPI_Abort( comm, INSUFFICIENT_MEMORY );
}
fprintf( stderr, "p%d: allocated dbond list: num_dbonds=%d space=%ldMB\n",
system->my_rank, bond_cap*MAX_BONDS*3,
bond_cap*MAX_BONDS*3*sizeof(dbond_data)/(1024*1024) );
#endif
free( hb_top );
free( bond_top );
return SUCCESS;
}
#elif defined(LAMMPS_REAX)
int Init_Lists( reax_system *system, control_params *control,
simulation_data *data, storage *workspace, reax_list **lists,
mpi_datatypes *mpi_data, char *msg )
{
int i, num_nbrs;
int total_hbonds, total_bonds, bond_cap, num_3body, cap_3body, Htop;
int *hb_top, *bond_top;
int nrecv[MAX_NBRS];
MPI_Comm comm;
int mincap = system->mincap;
double safezone = system->safezone;
double saferzone = system->saferzone;
comm = mpi_data->world;
bond_top = (int*) calloc( system->total_cap, sizeof(int) );
hb_top = (int*) calloc( system->local_cap, sizeof(int) );
Estimate_Storages( system, control, lists,
&Htop, hb_top, bond_top, &num_3body, comm );
if( control->hbond_cut > 0 ) {
/* init H indexes */
total_hbonds = 0;
for( i = 0; i < system->n; ++i ) {
system->my_atoms[i].num_hbonds = hb_top[i];
total_hbonds += hb_top[i];
}
total_hbonds = (int)(MAX( total_hbonds*saferzone, mincap*MIN_HBONDS ));
if( !Make_List( system->Hcap, total_hbonds, TYP_HBOND,
*lists+HBONDS, comm ) ) {
fprintf( stderr, "not enough space for hbonds list. terminating!\n" );
MPI_Abort( comm, INSUFFICIENT_MEMORY );
}
#if defined(DEBUG_FOCUS)
fprintf( stderr, "p%d: allocated hbonds: total_hbonds=%d, space=%dMB\n",
system->my_rank, total_hbonds,
(int)(total_hbonds*sizeof(hbond_data)/(1024*1024)) );
#endif
}
/* bonds list */
//Allocate_Bond_List( system->N, bond_top, (*lists)+BONDS );
//num_bonds = bond_top[system->N-1];
total_bonds = 0;
for( i = 0; i < system->N; ++i ) {
system->my_atoms[i].num_bonds = bond_top[i];
total_bonds += bond_top[i];
}
bond_cap = (int)(MAX( total_bonds*safezone, mincap*MIN_BONDS ));
if( !Make_List( system->total_cap, bond_cap, TYP_BOND,
*lists+BONDS, comm ) ) {
fprintf( stderr, "not enough space for bonds list. terminating!\n" );
MPI_Abort( comm, INSUFFICIENT_MEMORY );
}
#if defined(DEBUG_FOCUS)
fprintf( stderr, "p%d: allocated bonds: total_bonds=%d, space=%dMB\n",
system->my_rank, bond_cap,
(int)(bond_cap*sizeof(bond_data)/(1024*1024)) );
#endif
/* 3bodies list */
cap_3body = (int)(MAX( num_3body*safezone, MIN_3BODIES ));
if( !Make_List( bond_cap, cap_3body, TYP_THREE_BODY,
*lists+THREE_BODIES, comm ) ){
fprintf( stderr, "Problem in initializing angles list. Terminating!\n" );
MPI_Abort( comm, INSUFFICIENT_MEMORY );
}
#if defined(DEBUG_FOCUS)
fprintf( stderr, "p%d: allocated 3-body list: num_3body=%d, space=%dMB\n",
system->my_rank, cap_3body,
(int)(cap_3body*sizeof(three_body_interaction_data)/(1024*1024)) );
#endif
#if defined(TEST_FORCES)
if( !Make_List( system->total_cap, bond_cap*8, TYP_DDELTA,
*lists+DDELTAS, comm ) ) {
fprintf( stderr, "Problem in initializing dDelta list. Terminating!\n" );
MPI_Abort( comm, INSUFFICIENT_MEMORY );
}
fprintf( stderr, "p%d: allocated dDelta list: num_ddelta=%d space=%ldMB\n",
system->my_rank, bond_cap*30,
bond_cap*8*sizeof(dDelta_data)/(1024*1024) );
if( !Make_List( bond_cap, bond_cap*50, TYP_DBO, (*lists)+DBOS, comm ) ) {
fprintf( stderr, "Problem in initializing dBO list. Terminating!\n" );
MPI_Abort( comm, INSUFFICIENT_MEMORY );
}
fprintf( stderr, "p%d: allocated dbond list: num_dbonds=%d space=%ldMB\n",
system->my_rank, bond_cap*MAX_BONDS*3,
bond_cap*MAX_BONDS*3*sizeof(dbond_data)/(1024*1024) );
#endif
free( hb_top );
free( bond_top );
return SUCCESS;
}
#endif
#if defined(PURE_REAX)
void Initialize( reax_system *system, control_params *control,
simulation_data *data, storage *workspace,
reax_list **lists, output_controls *out_control,
mpi_datatypes *mpi_data )
{
char msg[MAX_STR];
if( Init_MPI_Datatypes( system, workspace, mpi_data, MPI_COMM_WORLD, msg ) ==
FAILURE ) {
fprintf( stderr, "p%d: init_mpi_datatypes: could not create datatypes\n",
system->my_rank );
fprintf( stderr, "p%d: mpi_data couldn't be initialized! terminating.\n",
system->my_rank );
MPI_Abort( mpi_data->world, CANNOT_INITIALIZE );
}
#if defined(DEBUG)
fprintf( stderr, "p%d: initialized mpi datatypes\n", system->my_rank );
#endif
if( Init_System(system, control, data, workspace, mpi_data, msg) == FAILURE ){
fprintf( stderr, "p%d: %s\n", system->my_rank, msg );
fprintf( stderr, "p%d: system could not be initialized! terminating.\n",
system->my_rank );
MPI_Abort( mpi_data->world, CANNOT_INITIALIZE );
}
#if defined(DEBUG)
fprintf( stderr, "p%d: system initialized\n", system->my_rank );
#endif
if( Init_Simulation_Data(system, control, data, mpi_data, msg) == FAILURE ) {
fprintf( stderr, "p%d: %s\n", system->my_rank, msg );
fprintf( stderr, "p%d: sim_data couldn't be initialized! terminating.\n",
system->my_rank );
MPI_Abort( mpi_data->world, CANNOT_INITIALIZE );
}
#if defined(DEBUG)
fprintf( stderr, "p%d: initialized simulation data\n", system->my_rank );
#endif
if( Init_Workspace( system, control, workspace, mpi_data->world, msg ) ==
FAILURE ) {
fprintf( stderr, "p%d:init_workspace: not enough memory\n",
system->my_rank );
fprintf( stderr, "p%d:workspace couldn't be initialized! terminating.\n",
system->my_rank );
MPI_Abort( mpi_data->world, CANNOT_INITIALIZE );
}
#if defined(DEBUG)
fprintf( stderr, "p%d: initialized workspace\n", system->my_rank );
#endif
if( Init_Lists( system, control, data, workspace, lists, mpi_data, msg ) ==
FAILURE ) {
fprintf( stderr, "p%d: %s\n", system->my_rank, msg );
fprintf( stderr, "p%d: system could not be initialized! terminating.\n",
system->my_rank );
MPI_Abort( mpi_data->world, CANNOT_INITIALIZE );
}
#if defined(DEBUG)
fprintf( stderr, "p%d: initialized lists\n", system->my_rank );
#endif
if(Init_Output_Files(system,control,out_control,mpi_data,msg) == FAILURE) {
fprintf( stderr, "p%d: %s\n", system->my_rank, msg );
fprintf( stderr, "p%d: could not open output files! terminating...\n",
system->my_rank );
MPI_Abort( mpi_data->world, CANNOT_INITIALIZE );
}
#if defined(DEBUG)
fprintf( stderr, "p%d: output files opened\n", system->my_rank );
#endif
if( control->tabulate ) {
if( Init_Lookup_Tables(system,control,workspace,mpi_data,msg) == FAILURE ) {
fprintf( stderr, "p%d: %s\n", system->my_rank, msg );
fprintf( stderr, "p%d: couldn't create lookup table! terminating.\n",
system->my_rank );
MPI_Abort( mpi_data->world, CANNOT_INITIALIZE );
}
#if defined(DEBUG)
fprintf( stderr, "p%d: initialized lookup tables\n", system->my_rank );
#endif
}
Init_Force_Functions( control );
#if defined(DEBUG)
fprintf( stderr, "p%d: initialized force functions\n", system->my_rank );
#endif
/*#ifdef TEST_FORCES
Init_Force_Test_Functions();
fprintf(stderr,"p%d: initialized force test functions\n",system->my_rank);
#endif */
}
#elif defined(LAMMPS_REAX)
void Initialize( reax_system *system, control_params *control,
simulation_data *data, storage *workspace,
reax_list **lists, output_controls *out_control,
mpi_datatypes *mpi_data, MPI_Comm comm )
{
char msg[MAX_STR];
if( Init_MPI_Datatypes(system, workspace, mpi_data, comm, msg) == FAILURE ) {
fprintf( stderr, "p%d: init_mpi_datatypes: could not create datatypes\n",
system->my_rank );
fprintf( stderr, "p%d: mpi_data couldn't be initialized! terminating.\n",
system->my_rank );
MPI_Abort( mpi_data->world, CANNOT_INITIALIZE );
}
#if defined(DEBUG)
fprintf( stderr, "p%d: initialized mpi datatypes\n", system->my_rank );
#endif
if( Init_System(system, control, msg) == FAILURE ){
fprintf( stderr, "p%d: %s\n", system->my_rank, msg );
fprintf( stderr, "p%d: system could not be initialized! terminating.\n",
system->my_rank );
MPI_Abort( mpi_data->world, CANNOT_INITIALIZE );
}
#if defined(DEBUG)
fprintf( stderr, "p%d: system initialized\n", system->my_rank );
#endif
if( Init_Simulation_Data( system, control, data, msg ) == FAILURE ) {
fprintf( stderr, "p%d: %s\n", system->my_rank, msg );
fprintf( stderr, "p%d: sim_data couldn't be initialized! terminating.\n",
system->my_rank );
MPI_Abort( mpi_data->world, CANNOT_INITIALIZE );
}
#if defined(DEBUG)
fprintf( stderr, "p%d: initialized simulation data\n", system->my_rank );
#endif
if( Init_Workspace( system, control, workspace, mpi_data->world, msg ) ==
FAILURE ) {
fprintf( stderr, "p%d:init_workspace: not enough memory\n",
system->my_rank );
fprintf( stderr, "p%d:workspace couldn't be initialized! terminating.\n",
system->my_rank );
MPI_Abort( mpi_data->world, CANNOT_INITIALIZE );
}
#if defined(DEBUG)
fprintf( stderr, "p%d: initialized workspace\n", system->my_rank );
#endif
if( Init_Lists( system, control, data, workspace, lists, mpi_data, msg ) ==
FAILURE ) {
fprintf( stderr, "p%d: %s\n", system->my_rank, msg );
fprintf( stderr, "p%d: system could not be initialized! terminating.\n",
system->my_rank );
MPI_Abort( mpi_data->world, CANNOT_INITIALIZE );
}
#if defined(DEBUG)
fprintf( stderr, "p%d: initialized lists\n", system->my_rank );
#endif
if( Init_Output_Files(system,control,out_control,mpi_data,msg)== FAILURE) {
fprintf( stderr, "p%d: %s\n", system->my_rank, msg );
fprintf( stderr, "p%d: could not open output files! terminating...\n",
system->my_rank );
MPI_Abort( mpi_data->world, CANNOT_INITIALIZE );
}
#if defined(DEBUG)
fprintf( stderr, "p%d: output files opened\n", system->my_rank );
#endif
if( control->tabulate ) {
if( Init_Lookup_Tables( system, control, workspace, mpi_data, msg ) == FAILURE ) {
fprintf( stderr, "p%d: %s\n", system->my_rank, msg );
fprintf( stderr, "p%d: couldn't create lookup table! terminating.\n",
system->my_rank );
MPI_Abort( mpi_data->world, CANNOT_INITIALIZE );
}
#if defined(DEBUG)
fprintf( stderr, "p%d: initialized lookup tables\n", system->my_rank );
#endif
}
Init_Force_Functions( control );
#if defined(DEBUG)
fprintf( stderr, "p%d: initialized force functions\n", system->my_rank );
#endif
/*#if defined(TEST_FORCES)
Init_Force_Test_Functions();
fprintf(stderr,"p%d: initialized force test functions\n",system->my_rank);
#endif*/
}
#endif

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