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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@7454 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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This commit is contained in:
sjplimp
2012-01-06 20:40:29 +00:00
parent aee60101d1
commit cf4145cfe5
19 changed files with 236 additions and 48 deletions
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8
src/USER-REAXC/Install.sh
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@ -5,10 +5,14 @@ if (test $1 = 1) then
cp -p pair_reax_c.cpp ..
cp -p fix_qeq_reax.cpp ..
cp -p fix_reax_c.cpp ..
cp -p fix_reaxc_bonds.cpp ..
cp -p fix_reaxc_species.cpp ..
cp -p pair_reax_c.h ..
cp -p fix_qeq_reax.h ..
cp -p fix_reax_c.h ..
cp -p fix_reaxc_bonds.h ..
cp -p fix_reaxc_species.h ..
cp -p reaxc_allocate.cpp ..
cp -p reaxc_basic_comm.cpp ..
@ -61,10 +65,14 @@ elif (test $1 = 0) then
rm -f ../pair_reax_c.cpp
rm -f ../fix_qeq_reax.cpp
rm -f ../fix_reax_c.cpp
rm -f ../fix_reaxc_bonds.cpp
rm -f ../fix_reaxc_species.cpp
rm -f ../pair_reax_c.h
rm -f ../fix_qeq_reax.h
rm -f ../fix_reax_c.h
rm -f ../fix_reaxc_bonds.h
rm -f ../fix_reaxc_species.h
rm -f ../reaxc_allocate.cpp
rm -f ../reaxc_basic_comm.cpp

32
src/USER-REAXC/pair_reax_c.cpp
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@ -47,6 +47,8 @@
#include "reaxc_reset_tools.h"
#include "reaxc_traj.h"
#include "reaxc_vector.h"
#include "fix_reaxc_bonds.h"
#include "fix_reaxc_species.h"
using namespace LAMMPS_NS;
@ -167,7 +169,7 @@ void PairReaxC::allocate( )
void PairReaxC::settings(int narg, char **arg)
{
if (narg != 1 && narg != 3) error->all(FLERR,"Illegal pair_style command");
if (narg < 1) error->all(FLERR,"Illegal pair_style command");
// read name of control file or use default controls
@ -194,6 +196,7 @@ void PairReaxC::settings(int narg, char **arg)
// default values
qeqflag = 1;
control->lgflag = 0;
// process optional keywords
@ -206,6 +209,12 @@ void PairReaxC::settings(int narg, char **arg)
else if (strcmp(arg[iarg+1],"no") == 0) qeqflag = 0;
else error->all(FLERR,"Illegal pair_style reax/c command");
iarg += 2;
} else if (strcmp(arg[iarg],"lgvdw") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal pair_style reax/c command");
if (strcmp(arg[iarg+1],"yes") == 0) control->lgflag = 1;
else if (strcmp(arg[iarg+1],"no") == 0) control->lgflag = 0;
else error->all(FLERR,"Illegal pair_style reax/c command");
iarg += 2;
} else error->all(FLERR,"Illegal pair_style reax/c command");
}
@ -400,6 +409,13 @@ void PairReaxC::compute(int eflag, int vflag)
if (eflag || vflag) ev_setup(eflag,vflag);
else evflag = vflag_fdotr = eflag_global = vflag_global = 0;
/* if ((eflag_atom || vflag_atom) && firstwarn) {
firstwarn = 0;
if (comm->me == 0)
error->warning(FLERR,"Pair reax/c cannot yet compute "
"per-atom energy or stress");
} */
if (vflag_global) control->virial = 1;
else control->virial = 0;
@ -411,10 +427,6 @@ void PairReaxC::compute(int eflag, int vflag)
system->big_box.box_norms[0] = 0;
system->big_box.box_norms[1] = 0;
system->big_box.box_norms[2] = 0;
system->evflag = evflag;
system->vflag_atom = vflag_atom;
if( comm->me == 0 ) t_start = MPI_Wtime();
// setup data structures
@ -494,6 +506,12 @@ void PairReaxC::compute(int eflag, int vflag)
Output_Results( system, control, data, &lists, out_control, mpi_data );
if(fixbond_flag)
fixbond( system, control, data, &lists, out_control, mpi_data );
if(fixspecies_flag)
fixspecies( system, control, data, &lists, out_control, mpi_data );
}
/* ---------------------------------------------------------------------- */
@ -745,7 +763,7 @@ void PairReaxC::read_reax_forces()
/* ---------------------------------------------------------------------- */
void *PairReaxC::extract(const char *str, int &dim)
void *PairReaxC::extract(char *str, int &dim)
{
dim = 1;
if (strcmp(str,"chi") == 0 && chi) {
@ -768,3 +786,5 @@ void *PairReaxC::extract(const char *str, int &dim)
}
return NULL;
}
/* ---------------------------------------------------------------------- */

9
src/USER-REAXC/pair_reax_c.h
View File

@ -45,16 +45,17 @@ class PairReaxC : public Pair {
void init_style();
double init_one(int, int);
void *extract(char *, int &);
int fixbond_flag, fixspecies_flag;
private:
reax_system *system;
control_params *control;
reax_system *system;
output_controls *out_control;
simulation_data *data;
storage *workspace;
reax_list *lists;
output_controls *out_control;
mpi_datatypes *mpi_data;
private:
double cutmax;
int *map;
class FixReaxC *fix_reax;

1
src/USER-REAXC/reaxc_allocate.cpp
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@ -92,6 +92,7 @@ inline void reax_atom_Copy( reax_atom *dest, reax_atom *src )
dest->Hindex = src->Hindex;
dest->num_bonds = src->num_bonds;
dest->num_hbonds = src->num_hbonds;
dest->numbonds = src->numbonds;
}

6
src/USER-REAXC/reaxc_bond_orders.cpp
View File

@ -596,7 +596,7 @@ void Add_dBond_to_Forces( reax_system *system, int i, int pj,
rvec_ScaledAdd( workspace->f[k], -coef.C3dbopi2, nbr_k->bo_data.dBOp );
// tally into per-atom virial
if( system->vflag_atom ) {
if( system->pair_ptr->vflag_atom ) {
f_scaler = -(coef.C2dbo + coef.C2dDelta + coef.C3dbopi + coef.C3dbopi2);
rvec_Scale( fk_tmp, -f_scaler, nbr_k->bo_data.dBOp);
system->pair_ptr->v_tally(k, fk_tmp);
@ -642,7 +642,7 @@ void Add_dBond_to_Forces( reax_system *system, int i, int pj,
rvec_ScaledAdd( workspace->f[k], -coef.C4dbopi2, nbr_k->bo_data.dBOp );
// tally into per-atom virial
if( system->vflag_atom ) {
if( system->pair_ptr->vflag_atom ) {
f_scaler = -(coef.C3dbo + coef.C3dDelta + coef.C4dbopi + coef.C4dbopi2);
rvec_Scale( fk_tmp, -f_scaler, nbr_k->bo_data.dBOp);
system->pair_ptr->v_tally(k, fk_tmp);
@ -673,7 +673,7 @@ void Add_dBond_to_Forces( reax_system *system, int i, int pj,
/*3rd, dBOpi2*/
rvec_ScaledAdd( workspace->f[j], coef.C4dbopi2, workspace->dDeltap_self[j] );
if( system->vflag_atom) {
if( system->pair_ptr->vflag_atom) {
// forces on i
f_scaler = coef.C1dbo + coef.C1dDelta + coef.C2dbopi + coef.C2dbopi2;

4
src/USER-REAXC/reaxc_bonds.cpp
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@ -93,7 +93,7 @@ void Bonds( reax_system *system, control_params *control,
-twbp->De_pp * bo_ij->BO_pi2;
/* tally into per-atom energy */
if( system->evflag)
if( system->pair_ptr->evflag)
system->pair_ptr->ev_tally(i,j,natoms,1,ebond,0.0,0.0,0.0,0.0,0.0);
/* calculate derivatives of Bond Orders */
@ -136,7 +136,7 @@ void Bonds( reax_system *system, control_params *control,
(gp3*exphub1 + 25.0*gp4*exphuov*hulpov*(exphua1+exphub1));
/* tally into per-atom energy */
if( system->evflag)
if( system->pair_ptr->evflag)
system->pair_ptr->ev_tally(i,j,natoms,1,estriph,0.0,0.0,0.0,0.0,0.0);
bo_ij->Cdbo += decobdbo;

1
src/USER-REAXC/reaxc_defs.h
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@ -104,6 +104,7 @@
#define MAX_ITR 10
#define RESTART 30
#define MAX_BOND 20
/******************* ENUMERATIONS *************************/

57
src/USER-REAXC/reaxc_ffield.cpp
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@ -25,6 +25,7 @@
----------------------------------------------------------------------*/
#include "pair_reax_c.h"
#include "error.h"
#if defined(PURE_REAX)
#include "ffield.h"
#include "tool_box.h"
@ -42,6 +43,8 @@ char Read_Force_Field( char *ffield_file, reax_interaction *reax,
char **tmp;
char ****tor_flag;
int c, i, j, k, l, m, n, o, p, cnt;
int lgflag = control->lgflag;
int errorflag = 1;
real val;
MPI_Comm comm;
@ -161,9 +164,10 @@ char Read_Force_Field( char *ffield_file, reax_interaction *reax,
reax->gp.vdw_type = 0;
/* reading single atom parameters */
/* there are 4 lines of each single atom parameters in ff files. these
parameters later determine some of the pair and triplet parameters using
combination rules. */
/* there are 4 or 5 lines of each single atom parameters in ff files,
depending on using lgvdw or not. These parameters later determine
some of the pair and triplet parameters using combination rules. */
for( i = 0; i < reax->num_atom_types; i++ ) {
/* line one */
fgets( s, MAX_LINE, fp );
@ -211,7 +215,13 @@ char Read_Force_Field( char *ffield_file, reax_interaction *reax,
/* line 4 */
fgets( s, MAX_LINE, fp );
c = Tokenize( s, &tmp );
/* Sanity check */
if (c < 3) {
fprintf(stderr, "Inconsistent ffield file (reaxc_ffield.cpp) \n");
MPI_Abort( comm, FILE_NOT_FOUND );
}
val = atof(tmp[0]); reax->sbp[i].p_ovun2 = val;
val = atof(tmp[1]); reax->sbp[i].p_val3 = val;
val = atof(tmp[2]);
@ -220,18 +230,35 @@ char Read_Force_Field( char *ffield_file, reax_interaction *reax,
val = atof(tmp[5]); reax->sbp[i].rcore2 = val;
val = atof(tmp[6]); reax->sbp[i].ecore2 = val;
val = atof(tmp[7]); reax->sbp[i].acore2 = val;
/* line 5, only if lgvdw is yes */
if (lgflag) {
fgets( s, MAX_LINE, fp );
c = Tokenize( s, &tmp );
/* Sanity check */
if (c > 3) {
fprintf(stderr, "Inconsistent ffield file (reaxc_ffield.cpp) \n");
MPI_Abort( comm, FILE_NOT_FOUND );
}
val = atof(tmp[0]); reax->sbp[i].lgcij = val;
val = atof(tmp[1]); reax->sbp[i].lgre = val;
}
if( reax->sbp[i].rcore2>0.01 && reax->sbp[i].acore2>0.01 ){ // Inner-wall
if( reax->sbp[i].gamma_w>0.5 ){ // Shielding vdWaals
if( reax->gp.vdw_type != 0 && reax->gp.vdw_type != 3 )
fprintf( stderr, "Warning: inconsistent vdWaals-parameters\n" \
if( reax->gp.vdw_type != 0 && reax->gp.vdw_type != 3 ) {
if (errorflag)
fprintf( stderr, "Warning: inconsistent vdWaals-parameters\n" \
"Force field parameters for element %s\n" \
"indicate inner wall+shielding, but earlier\n" \
"atoms indicate different vdWaals-method.\n" \
"This may cause division-by-zero errors.\n" \
"Keeping vdWaals-setting for earlier atoms.\n",
reax->sbp[i].name );
errorflag = 0;
}
else{
reax->gp.vdw_type = 3;
#if defined(DEBUG)
@ -439,6 +466,7 @@ char Read_Force_Field( char *ffield_file, reax_interaction *reax,
reax->sbp[i].gamma,-1.5);
// additions for additional vdWaals interaction types - inner core
reax->tbp[i][j].rcore = reax->tbp[j][i].rcore =
sqrt( reax->sbp[i].rcore2 * reax->sbp[j].rcore2 );
@ -447,6 +475,15 @@ char Read_Force_Field( char *ffield_file, reax_interaction *reax,
reax->tbp[i][j].acore = reax->tbp[j][i].acore =
sqrt( reax->sbp[i].acore2 * reax->sbp[j].acore2 );
// additions for additional vdWalls interaction types lg correction
reax->tbp[i][j].lgcij = reax->tbp[j][i].lgcij =
sqrt( reax->sbp[i].lgcij * reax->sbp[j].lgcij );
reax->tbp[i][j].lgre = reax->tbp[j][i].lgre = 2.0 *
sqrt( reax->sbp[i].lgre*reax->sbp[j].lgre );
}
@ -500,6 +537,12 @@ char Read_Force_Field( char *ffield_file, reax_interaction *reax,
reax->tbp[j][k].r_pp = val;
reax->tbp[k][j].r_pp = val;
}
val = atof(tmp[8]);
if (val >= 0.0) {
reax->tbp[j][k].lgcij = val;
reax->tbp[k][j].lgcij = val;
}
}
}

4
src/USER-REAXC/reaxc_hydrogen_bonds.cpp
View File

@ -146,8 +146,6 @@ void Hydrogen_Bonds( reax_system *system, control_params *control,
CEhb3 = -hbp->p_hb3 *
(-hbp->r0_hb / SQR(r_jk) + 1.0 / hbp->r0_hb) * e_hb;
fprintf(stderr," H bond called \n");
/*fprintf( stdout,
"%6d%6d%6d%12.6f%12.6f%12.6f%12.6f%12.6f%12.6f%12.6f%12.6f%12.6f\n",
system->my_atoms[i].orig_id, system->my_atoms[j].orig_id,
@ -192,7 +190,7 @@ void Hydrogen_Bonds( reax_system *system, control_params *control,
}
/* tally into per-atom virials */
if (system->vflag_atom || system->evflag) {
if (system->pair_ptr->vflag_atom || system->pair_ptr->evflag) {
rvec_ScaledSum( delij, 1., system->my_atoms[i].x,
-1., system->my_atoms[j].x );
rvec_ScaledSum( delkj, 1., system->my_atoms[k].x,

65
src/USER-REAXC/reaxc_io_tools.cpp
View File

@ -25,6 +25,7 @@
----------------------------------------------------------------------*/
#include "pair_reax_c.h"
#include "update.h"
#if defined(PURE_REAX)
#include "io_tools.h"
#include "basic_comm.h"
@ -1030,6 +1031,70 @@ void Print_Total_Force( reax_system *system, simulation_data *data,
workspace->f[i][0], workspace->f[i][1], workspace->f[i][2] );
}
void fixbond( reax_system *system, control_params *control,
simulation_data *data, reax_list **lists,
output_controls *out_control, mpi_datatypes *mpi_data )
{
// count the number of bonds around each atom, for fix reax/c/bond
int i, j, pj, my_bonds_0, i_id, j_id;
int my_bonds_max = 0;
double BO_tmp;
control->bg_cut = 0.3; // this values will not change with control file
reax_list *bonds = (*lists) + BONDS;
for( i=0; i < system->n; ++i ) {
my_bonds_0 = 0;
i_id = system->my_atoms[i].orig_id; // orig_id is atom->tag
for( pj = Start_Index(i, bonds); pj < End_Index(i, bonds); ++pj ) {
j = bonds->select.bond_list[pj].nbr;
j_id = system->my_atoms[j].orig_id;
BO_tmp = bonds->select.bond_list[pj].bo_data.BO;
if( i_id != j_id && BO_tmp >= control->bg_cut ) {
++my_bonds_0;
system->my_atoms[i].nbr_id[my_bonds_0] = j_id;
system->my_atoms[i].nbr_bo[my_bonds_0] = BO_tmp;
}
}
my_bonds_max = MAX(my_bonds_0, my_bonds_max);
system->my_atoms[i].numbonds = my_bonds_0;
system->my_bonds = my_bonds_max;
}
}
void fixspecies( reax_system *system, control_params *control,
simulation_data *data, reax_list **lists,
output_controls *out_control, mpi_datatypes *mpi_data )
{
// count the number of bonds around each atom, for fix reax/c/bond
int i, j, pj, my_bonds_0, i_id, j_id;
int my_bonds_max = 0;
double BO_tmp;
control->bg_cut = 0.3; // this values will not change with control file
reax_list *bonds = (*lists) + BONDS;
for( i=0; i < system->n; ++i ) {
my_bonds_0 = 0;
i_id = system->my_atoms[i].orig_id;
for( pj = Start_Index(i, bonds); pj < End_Index(i, bonds); ++pj ) {
j = bonds->select.bond_list[pj].nbr;
j_id = system->my_atoms[j].orig_id;
BO_tmp = bonds->select.bond_list[pj].bo_data.BO;
if( i_id != j_id && BO_tmp >= control->bg_cut ) {
++my_bonds_0;
system->my_atoms[i].nbr_id[my_bonds_0] = j_id;
system->my_atoms[i].nbr_bo[my_bonds_0] = BO_tmp;
}
}
my_bonds_max = MAX(my_bonds_0, my_bonds_max);
system->my_atoms[i].numbonds = my_bonds_0;
system->my_bonds = my_bonds_max;
}
}
void Output_Results( reax_system *system, control_params *control,
simulation_data *data, reax_list **lists,
output_controls *out_control, mpi_datatypes *mpi_data )

4
src/USER-REAXC/reaxc_io_tools.h
View File

@ -56,6 +56,10 @@ void Print_Bond_List2( reax_system*, reax_list*, char* );
void Print_Total_Force( reax_system*, simulation_data*, storage* );
void Output_Results( reax_system*, control_params*, simulation_data*,
reax_list**, output_controls*, mpi_datatypes* );
void fixbond( reax_system*, control_params*, simulation_data*,
reax_list**, output_controls*, mpi_datatypes* );
void fixspecies( reax_system*, control_params*, simulation_data*,
reax_list**, output_controls*, mpi_datatypes* );
#if defined(DEBUG_FOCUS) || defined(TEST_FORCES) || defined(TEST_ENERGY)
void Debug_Marker_Bonded( output_controls*, int );

2
src/USER-REAXC/reaxc_lookup.cpp
View File

@ -266,7 +266,7 @@ int Init_Lookup_Tables( reax_system *system, control_params *control,
"lookup:LR[i,j].CEclmb", comm );
for( r = 1; r <= control->tabulate; ++r ) {
LR_vdW_Coulomb( system, workspace, i, j, r * dr, &(LR[i][j].y[r]) );
LR_vdW_Coulomb( system, workspace, control, i, j, r * dr, &(LR[i][j].y[r]) );
h[r] = LR[i][j].dx;
fh[r] = LR[i][j].y[r].H;
fvdw[r] = LR[i][j].y[r].e_vdW;

6
src/USER-REAXC/reaxc_multi_body.cpp
View File

@ -91,7 +91,7 @@ void Atom_Energy( reax_system *system, control_params *control,
workspace->CdDelta[i] += CElp; // lp - 1st term
/* tally into per-atom energy */
if( system->evflag)
if( system->pair_ptr->evflag)
system->pair_ptr->ev_tally(i,i,system->n,1,e_lp,0.0,0.0,0.0,0.0,0.0);
#ifdef TEST_ENERGY
@ -128,7 +128,7 @@ void Atom_Energy( reax_system *system, control_params *control,
workspace->CdDelta[i] += deahu2dsbo;
/* tally into per-atom energy */
if( system->evflag)
if( system->pair_ptr->evflag)
system->pair_ptr->ev_tally(i,j,system->n,1,e_lph,0.0,0.0,0.0,0.0,0.0);
#ifdef TEST_ENERGY
@ -219,7 +219,7 @@ void Atom_Energy( reax_system *system, control_params *control,
p_ovun4 * exp_ovun1 * SQR(inv_exp_ovun1) + CEunder2;
/* tally into per-atom energy */
if( system->evflag) {
if( system->pair_ptr->evflag) {
eng_tmp = e_ov + e_un;
f_tmp = CEover3 + CEunder3;
system->pair_ptr->ev_tally(i,i,system->n,1,eng_tmp,0.0,0.0,0.0,0.0,0.0);

41
src/USER-REAXC/reaxc_nonbonded.cpp
View File

@ -50,6 +50,7 @@ void vdW_Coulomb_Energy( reax_system *system, control_params *control,
real Tap, dTap, dfn13, CEvd, CEclmb, de_core;
real dr3gamij_1, dr3gamij_3;
real e_ele, e_vdW, e_core, SMALL = 0.0001;
real e_lg, de_lg, r_ij5, r_ij6, re6;
rvec temp, ext_press;
two_body_parameters *twbp;
far_neighbor_data *nbr_pj;
@ -65,6 +66,7 @@ void vdW_Coulomb_Energy( reax_system *system, control_params *control,
p_vdW1i = 1.0 / p_vdW1;
e_core = 0;
e_vdW = 0;
e_lg = de_lg = 0.0;
for( i = 0; i < natoms; ++i ) {
start_i = Start_Index(i, far_nbrs);
@ -155,6 +157,19 @@ void vdW_Coulomb_Energy( reax_system *system, control_params *control,
de_core = -(twbp->acore/twbp->rcore) * e_core;
CEvd += dTap * e_core + Tap * de_core / r_ij;
// lg correction, only if lgvdw is yes
if (control->lgflag) {
r_ij5 = pow( r_ij, 5.0 );
r_ij6 = pow( r_ij, 6.0 );
re6 = pow( twbp->lgre, 6.0 );
e_lg = -(twbp->lgcij/( r_ij6 + re6 ));
data->my_en.e_vdW += Tap * e_lg;
de_lg = -6.0 * e_lg * r_ij5 / ( r_ij6 + re6 ) ;
CEvd += dTap * e_lg + Tap * de_lg / r_ij;
}
}
/*Coulomb Calculations*/
@ -169,8 +184,8 @@ void vdW_Coulomb_Energy( reax_system *system, control_params *control,
( dTap - Tap * r_ij / dr3gamij_1 ) / dr3gamij_3;
/* tally into per-atom energy */
if( system->evflag || system->vflag_atom) {
pe_vdw = Tap * (e_vdW + e_core);
if( system->pair_ptr->evflag || system->pair_ptr->vflag_atom) {
pe_vdw = Tap * (e_vdW + e_core + e_lg);
rvec_ScaledSum( delij, 1., system->my_atoms[i].x,
-1., system->my_atoms[j].x );
f_tmp = -(CEvd + CEclmb);
@ -334,7 +349,7 @@ void Tabulated_vdW_Coulomb_Energy( reax_system *system,control_params *control,
/* tally into per-atom energy */
if( system->evflag || system->vflag_atom) {
if( system->pair_ptr->evflag || system->pair_ptr->vflag_atom) {
rvec_ScaledSum( delij, 1., system->my_atoms[i].x,
-1., system->my_atoms[j].x );
f_tmp = -(CEvd + CEclmb);
@ -399,14 +414,13 @@ void Compute_Polarization_Energy( reax_system *system, simulation_data *data )
data->my_en.e_pol += en_tmp;
/* tally into per-atom energy */
if( system->evflag)
if( system->pair_ptr->evflag)
system->pair_ptr->ev_tally(i,i,system->n,1,0.0,en_tmp,0.0,0.0,0.0,0.0);
}
}
void LR_vdW_Coulomb( reax_system *system, storage *workspace,
int i, int j, real r_ij, LR_data *lr )
control_params *control, int i, int j, real r_ij, LR_data *lr )
{
real p_vdW1 = system->reax_param.gp.l[28];
real p_vdW1i = 1.0 / p_vdW1;
@ -415,11 +429,13 @@ void LR_vdW_Coulomb( reax_system *system, storage *workspace,
real Tap, dTap, dfn13;
real dr3gamij_1, dr3gamij_3;
real e_core, de_core;
real e_lg, de_lg, r_ij5, r_ij6, re6;
two_body_parameters *twbp;
twbp = &(system->reax_param.tbp[i][j]);
e_core = 0;
de_core = 0;
e_lg = de_lg = 0.0;
/* calculate taper and its derivative */
Tap = workspace->Tap[7] * r_ij + workspace->Tap[6];
@ -470,6 +486,19 @@ void LR_vdW_Coulomb( reax_system *system, storage *workspace,
de_core = -(twbp->acore/twbp->rcore) * e_core;
lr->CEvd += dTap * e_core + Tap * de_core / r_ij;
// lg correction, only if lgvdw is yes
if (control->lgflag) {
r_ij5 = pow( r_ij, 5.0 );
r_ij6 = pow( r_ij, 6.0 );
re6 = pow( twbp->lgre, 6.0 );
e_lg = -(twbp->lgcij/( r_ij6 + re6 ));
lr->e_vdW += Tap * e_lg;
de_lg = -6.0 * e_lg * r_ij5 / ( r_ij6 + re6 ) ;
lr->CEvd += dTap * e_lg + Tap * de_lg/r_ij;
}
}

3
src/USER-REAXC/reaxc_nonbonded.h
View File

@ -38,5 +38,6 @@ void Tabulated_vdW_Coulomb_Energy( reax_system*, control_params*,
void Compute_Polarization_Energy( reax_system*, simulation_data* );
void LR_vdW_Coulomb( reax_system*, storage*, int, int, real, LR_data* );
void LR_vdW_Coulomb( reax_system*, storage*, control_params*,
int, int, real, LR_data* );
#endif

6
src/USER-REAXC/reaxc_torsion_angles.cpp
View File

@ -484,7 +484,7 @@ void Torsion_Angles( reax_system *system, control_params *control,
}
/* tally into per-atom virials */
if( system->vflag_atom || system->evflag) {
if( system->pair_ptr->vflag_atom || system->pair_ptr->evflag) {
// acquire vectors
rvec_ScaledSum( delil, 1., system->my_atoms[l].x,
@ -509,9 +509,9 @@ void Torsion_Angles( reax_system *system, control_params *control,
// tally
eng_tmp = e_tor + e_con;
if( system->evflag)
if( system->pair_ptr->evflag)
system->pair_ptr->ev_tally(j,k,natoms,1,eng_tmp,0.0,0.0,0.0,0.0,0.0);
if( system->vflag_atom)
if( system->pair_ptr->vflag_atom)
system->pair_ptr->v_tally4(i,j,k,l,fi_tmp,fj_tmp,fk_tmp,delil,deljl,delkl);
}

9
src/USER-REAXC/reaxc_traj.cpp
View File

@ -815,6 +815,7 @@ int Write_Bonds(reax_system *system, control_params *control, reax_list *bonds,
bonds->select.bond_list[pj].bo_data.BO >= control->bg_cut )
++my_bonds;
}
/* allreduce - total number of bonds */
MPI_Allreduce( &my_bonds, &num_bonds, 1, MPI_INT, MPI_SUM, mpi_data->world );
@ -828,10 +829,11 @@ int Write_Bonds(reax_system *system, control_params *control, reax_list *bonds,
Reallocate_Output_Buffer( out_control, buffer_req, mpi_data->world );
/* fill in the buffer */
my_bonds = 0;
out_control->line[0] = 0;
out_control->buffer[0] = 0;
for( i=0; i < system->n; ++i )
my_bonds = 0;
for( i=0; i < system->n; ++i ) {
for( pj = Start_Index(i, bonds); pj < End_Index(i, bonds); ++pj ) {
bo_ij = &( bonds->select.bond_list[pj] );
j = bo_ij->nbr;
@ -854,12 +856,13 @@ int Write_Bonds(reax_system *system, control_params *control, reax_list *bonds,
fprintf(stderr, "write_traj_bonds: FATAL! invalid bond_info option");
MPI_Abort( mpi_data->world, UNKNOWN_OPTION );
}
strncpy( out_control->buffer + my_bonds*line_len,
out_control->line, line_len+1 );
++my_bonds;
}
}
}
#if defined(PURE_REAX)
if( out_control->traj_method == MPI_TRAJ ) {

20
src/USER-REAXC/reaxc_types.h
View File

@ -57,6 +57,7 @@
#define REAX_MAX_4BODY_PARAM 5
#define REAX_MAX_ATOM_TYPES 25
#define REAX_MAX_MOLECULE_SIZE 20
#define MAX_BOND 20 // same as reaxc_defs.h
/********************** TYPE DEFINITIONS ********************/
typedef int ivec[3];
@ -246,6 +247,11 @@ typedef struct
real rcore2;
real ecore2;
real acore2;
/* Line five in the ffield file, only for lgvdw yes */
real lgcij;
real lgre;
} single_body_parameters;
@ -270,6 +276,7 @@ typedef struct {
real r_vdW;
real gamma_w;
real rcore, ecore, acore;
real lgcij, lgre;
/* electrostatic parameters */
real gamma; // note: this parameter is gamma^-3 and not gamma.
@ -359,6 +366,11 @@ typedef struct
int num_bonds;
int num_hbonds;
int renumber;
int numbonds; // true number of bonds around atoms
int nbr_id[MAX_BOND]; // ids of neighbors around atoms
double nbr_bo[MAX_BOND]; // BO values of bond between i and nbr
double sum_bo, no_lp; // sum of BO values and no. of lone pairs
} reax_atom;
@ -472,12 +484,11 @@ typedef struct
simulation_box big_box, my_box, my_ext_box;
grid my_grid;
boundary_cutoff bndry_cuts;
reax_atom *my_atoms;
int evflag;
int vflag_atom;
class Pair *pair_ptr;
int my_bonds;
} reax_system;
@ -543,6 +554,9 @@ typedef struct
int diffusion_coef;
int freq_diffusion_coef;
int restrict_type;
int lgflag;
} control_params;

6
src/USER-REAXC/reaxc_valence_angles.cpp
View File

@ -416,7 +416,7 @@ void Valence_Angles( reax_system *system, control_params *control,
}
/* tally into per-atom virials */
if( system->vflag_atom || system->evflag) {
if( system->pair_ptr->vflag_atom || system->pair_ptr->evflag) {
/* Acquire vectors */
rvec_ScaledSum( delij, 1., system->my_atoms[i].x,
@ -430,9 +430,9 @@ void Valence_Angles( reax_system *system, control_params *control,
eng_tmp = e_ang + e_pen + e_coa;
if( system->evflag)
if( system->pair_ptr->evflag)
system->pair_ptr->ev_tally(j,j,system->N,1,eng_tmp,0.0,0.0,0.0,0.0,0.0);
if( system->vflag_atom)
if( system->pair_ptr->vflag_atom)
system->pair_ptr->v_tally3(i,j,k,fi_tmp,fk_tmp,delij,delkj);
}