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reaxc_types.h
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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/>.
----------------------------------------------------------------------*/
#ifndef __REAX_TYPES_H_
#define __REAX_TYPES_H_
#include "lmptype.h"
#include <ctype.h>
#include <math.h>
#include <mpi.h>
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include "sys/time.h"
#include <time.h>
#if defined LMP_USER_OMP
#define OMP_TIMING 1
#ifdef OMP_TIMING
// pkcoff timing fields
enum {
COMPUTEINDEX=0,
COMPUTEWLINDEX,
COMPUTEBFINDEX,
COMPUTEQEQINDEX,
COMPUTENBFINDEX,
COMPUTEIFINDEX,
COMPUTETFINDEX,
COMPUTEBOINDEX,
COMPUTEBONDSINDEX,
COMPUTEATOMENERGYINDEX,
COMPUTEVALENCEANGLESBOINDEX,
COMPUTETORSIONANGLESBOINDEX,
COMPUTEHBONDSINDEX,
COMPUTECG1INDEX,
COMPUTECG2INDEX,
COMPUTECGCOMPUTEINDEX,
COMPUTECALCQINDEX,
COMPUTEINITMVINDEX,
COMPUTEMVCOMPINDEX,
LASTTIMINGINDEX
};
extern double ompTimingData[LASTTIMINGINDEX];
extern int ompTimingCount[LASTTIMINGINDEX];
extern int ompTimingCGCount[LASTTIMINGINDEX];
#endif
#endif
/************* SOME DEFS - crucial for reax_types.h *********/
#define LAMMPS_REAX
//#define DEBUG
//#define DEBUG_FOCUS
//#define TEST_ENERGY
//#define TEST_FORCES
//#define CG_PERFORMANCE
//#define LOG_PERFORMANCE
//#define STANDARD_BOUNDARIES
//#define OLD_BOUNDARIES
//#define MIDPOINT_BOUNDARIES
#define REAX_MAX_STR 1024
#define REAX_MAX_NBRS 6
#define REAX_MAX_3BODY_PARAM 5
#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];
typedef double rvec[3];
typedef double rtensor[3][3];
typedef double rvec2[2];
typedef double rvec4[4];
// import LAMMPS' definition of tagint and bigint
typedef LAMMPS_NS::tagint rc_tagint;
typedef LAMMPS_NS::bigint rc_bigint;
typedef struct
{
int cnt;
int *index;
void *out_atoms;
} mpi_out_data;
typedef struct
{
MPI_Comm world;
MPI_Comm comm_mesh3D;
MPI_Datatype sys_info;
MPI_Datatype mpi_atom_type;
MPI_Datatype boundary_atom_type;
MPI_Datatype mpi_rvec, mpi_rvec2;
MPI_Datatype restart_atom_type;
MPI_Datatype header_line;
MPI_Datatype header_view;
MPI_Datatype init_desc_line;
MPI_Datatype init_desc_view;
MPI_Datatype atom_line;
MPI_Datatype atom_view;
MPI_Datatype bond_line;
MPI_Datatype bond_view;
MPI_Datatype angle_line;
MPI_Datatype angle_view;
mpi_out_data out_buffers[REAX_MAX_NBRS];
void *in1_buffer;
void *in2_buffer;
} mpi_datatypes;
typedef struct
{
int n_global;
double* l;
int vdw_type;
} global_parameters;
typedef struct
{
/* Line one in field file */
char name[15]; // Two character atom name
double r_s;
double valency; // Valency of the atom
double mass; // Mass of atom
double r_vdw;
double epsilon;
double gamma;
double r_pi;
double valency_e;
double nlp_opt;
/* Line two in field file */
double alpha;
double gamma_w;
double valency_boc;
double p_ovun5;
double chi;
double eta;
int p_hbond; // 1 for H, 2 for hbonding atoms (O,S,P,N), 0 for others
/* Line three in field file */
double r_pi_pi;
double p_lp2;
double b_o_131;
double b_o_132;
double b_o_133;
/* Line four in the field file */
double p_ovun2;
double p_val3;
double valency_val;
double p_val5;
double rcore2;
double ecore2;
double acore2;
/* Line five in the ffield file, only for lgvdw yes */
double lgcij;
double lgre;
} single_body_parameters;
/* Two Body Parameters */
typedef struct {
/* Bond Order parameters */
double p_bo1,p_bo2,p_bo3,p_bo4,p_bo5,p_bo6;
double r_s, r_p, r_pp; // r_o distances in BO formula
double p_boc3, p_boc4, p_boc5;
/* Bond Energy parameters */
double p_be1, p_be2;
double De_s, De_p, De_pp;
/* Over/Under coordination parameters */
double p_ovun1;
/* Van der Waal interaction parameters */
double D;
double alpha;
double r_vdW;
double gamma_w;
double rcore, ecore, acore;
double lgcij, lgre;
/* electrostatic parameters */
double gamma; // note: this parameter is gamma^-3 and not gamma.
double v13cor, ovc;
} two_body_parameters;
/* 3-body parameters */
typedef struct {
/* valence angle */
double theta_00;
double p_val1, p_val2, p_val4, p_val7;
/* penalty */
double p_pen1;
/* 3-body conjugation */
double p_coa1;
} three_body_parameters;
typedef struct{
int cnt;
three_body_parameters prm[REAX_MAX_3BODY_PARAM];
} three_body_header;
/* hydrogen-bond parameters */
typedef struct{
double r0_hb, p_hb1, p_hb2, p_hb3;
} hbond_parameters;
/* 4-body parameters */
typedef struct {
double V1, V2, V3;
/* torsion angle */
double p_tor1;
/* 4-body conjugation */
double p_cot1;
} four_body_parameters;
typedef struct
{
int cnt;
four_body_parameters prm[REAX_MAX_4BODY_PARAM];
} four_body_header;
typedef struct
{
int num_atom_types;
global_parameters gp;
single_body_parameters *sbp;
two_body_parameters **tbp;
three_body_header ***thbp;
hbond_parameters ***hbp;
four_body_header ****fbp;
} reax_interaction;
struct _reax_atom
{
rc_tagint orig_id;
int imprt_id;
int type;
char name[8];
rvec x; // position
rvec v; // velocity
rvec f; // force
rvec f_old;
double q; // charge
rvec4 s; // they take part in
rvec4 t; // computing q
int Hindex;
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
};
typedef _reax_atom reax_atom;
typedef struct
{
double V;
rvec min, max, box_norms;
rtensor box, box_inv;
rtensor trans, trans_inv;
rtensor g;
} simulation_box;
struct grid_cell
{
double cutoff;
rvec min, max;
ivec rel_box;
int mark;
int type;
int str;
int end;
int top;
int* atoms;
struct grid_cell** nbrs;
ivec* nbrs_x;
rvec* nbrs_cp;
};
typedef struct grid_cell grid_cell;
typedef struct
{
int total, max_atoms, max_nbrs;
ivec ncells;
rvec cell_len;
rvec inv_len;
ivec bond_span;
ivec nonb_span;
ivec vlist_span;
ivec native_cells;
ivec native_str;
ivec native_end;
double ghost_cut;
ivec ghost_span;
ivec ghost_nonb_span;
ivec ghost_hbond_span;
ivec ghost_bond_span;
grid_cell*** cells;
ivec *order;
} grid;
typedef struct
{
int rank;
int est_send, est_recv;
int atoms_str, atoms_cnt;
ivec rltv, prdc;
rvec bndry_min, bndry_max;
int send_type;
int recv_type;
ivec str_send;
ivec end_send;
ivec str_recv;
ivec end_recv;
} neighbor_proc;
typedef struct
{
int N;
int exc_gcells;
int exc_atoms;
} bound_estimate;
typedef struct
{
double ghost_nonb;
double ghost_hbond;
double ghost_bond;
double ghost_cutoff;
} boundary_cutoff;
using LAMMPS_NS::Pair;
struct _reax_system
{
reax_interaction reax_param;
rc_bigint bigN;
int n, N, numH;
int local_cap, total_cap, gcell_cap, Hcap;
int est_recv, est_trans, max_recved;
int wsize, my_rank, num_nbrs;
ivec my_coords;
neighbor_proc my_nbrs[REAX_MAX_NBRS];
int *global_offset;
simulation_box big_box, my_box, my_ext_box;
grid my_grid;
boundary_cutoff bndry_cuts;
reax_atom *my_atoms;
class Pair *pair_ptr;
int my_bonds;
int mincap;
double safezone, saferzone;
int omp_active;
};
typedef _reax_system reax_system;
/* system control parameters */
typedef struct
{
char sim_name[REAX_MAX_STR];
int nprocs;
int nthreads;
ivec procs_by_dim;
/* ensemble values:
0 : NVE
1 : bNVT (Berendsen)
2 : nhNVT (Nose-Hoover)
3 : sNPT (Parrinello-Rehman-Nose-Hoover) semiisotropic
4 : iNPT (Parrinello-Rehman-Nose-Hoover) isotropic
5 : NPT (Parrinello-Rehman-Nose-Hoover) Anisotropic*/
int ensemble;
int nsteps;
double dt;
int geo_format;
int restart;
int restrict_bonds;
int remove_CoM_vel;
int random_vel;
int reposition_atoms;
int reneighbor;
double vlist_cut;
double bond_cut;
double nonb_cut, nonb_low;
double hbond_cut;
double user_ghost_cut;
double bg_cut;
double bo_cut;
double thb_cut;
double thb_cutsq;
int tabulate;
int qeq_freq;
double q_err;
int refactor;
double droptol;
double T_init, T_final, T;
double Tau_T;
int T_mode;
double T_rate, T_freq;
int virial;
rvec P, Tau_P, Tau_PT;
int press_mode;
double compressibility;
int molecular_analysis;
int num_ignored;
int ignore[REAX_MAX_ATOM_TYPES];
int dipole_anal;
int freq_dipole_anal;
int diffusion_coef;
int freq_diffusion_coef;
int restrict_type;
int lgflag;
int enobondsflag;
} control_params;
typedef struct
{
double T;
double xi;
double v_xi;
double v_xi_old;
double G_xi;
} thermostat;
typedef struct
{
double P;
double eps;
double v_eps;
double v_eps_old;
double a_eps;
} isotropic_barostat;
typedef struct
{
rtensor P;
double P_scalar;
double eps;
double v_eps;
double v_eps_old;
double a_eps;
rtensor h0;
rtensor v_g0;
rtensor v_g0_old;
rtensor a_g0;
} flexible_barostat;
typedef struct
{
double start;
double end;
double elapsed;
double total;
double comm;
double nbrs;
double init_forces;
double bonded;
double nonb;
double qEq;
int s_matvecs;
int t_matvecs;
} reax_timing;
typedef struct
{
double e_tot;
double e_kin; // Total kinetic energy
double e_pot;
double e_bond; // Total bond energy
double e_ov; // Total over coordination
double e_un; // Total under coordination energy
double e_lp; // Total under coordination energy
double e_ang; // Total valance angle energy
double e_pen; // Total penalty energy
double e_coa; // Total three body conjgation energy
double e_hb; // Total Hydrogen bond energy
double e_tor; // Total torsional energy
double e_con; // Total four body conjugation energy
double e_vdW; // Total van der Waals energy
double e_ele; // Total electrostatics energy
double e_pol; // Polarization energy
} energy_data;
typedef struct
{
int step;
int prev_steps;
double time;
double M; // Total Mass
double inv_M; // 1 / Total Mass
rvec xcm; // Center of mass
rvec vcm; // Center of mass velocity
rvec fcm; // Center of mass force
rvec amcm; // Angular momentum of CoM
rvec avcm; // Angular velocity of CoM
double etran_cm; // Translational kinetic energy of CoM
double erot_cm; // Rotational kinetic energy of CoM
rtensor kinetic; // Kinetic energy tensor
rtensor virial; // Hydrodynamic virial
energy_data my_en;
energy_data sys_en;
double N_f; //Number of degrees of freedom
rvec t_scale;
rtensor p_scale;
thermostat therm; // Used in Nose_Hoover method
isotropic_barostat iso_bar;
flexible_barostat flex_bar;
double inv_W;
double kin_press;
rvec int_press;
rvec my_ext_press;
rvec ext_press;
rvec tot_press;
reax_timing timing;
} simulation_data;
typedef struct{
int thb;
int pthb; // pointer to the third body on the central atom's nbrlist
double theta, cos_theta;
rvec dcos_di, dcos_dj, dcos_dk;
} three_body_interaction_data;
typedef struct {
int nbr;
ivec rel_box;
double d;
rvec dvec;
} far_neighbor_data;
typedef struct {
int nbr;
int scl;
far_neighbor_data *ptr;
} hbond_data;
typedef struct{
int wrt;
rvec dVal;
} dDelta_data;
typedef struct{
int wrt;
rvec dBO, dBOpi, dBOpi2;
} dbond_data;
typedef struct{
double BO, BO_s, BO_pi, BO_pi2;
double Cdbo, Cdbopi, Cdbopi2;
double C1dbo, C2dbo, C3dbo;
double C1dbopi, C2dbopi, C3dbopi, C4dbopi;
double C1dbopi2, C2dbopi2, C3dbopi2, C4dbopi2;
rvec dBOp, dln_BOp_s, dln_BOp_pi, dln_BOp_pi2;
double *CdboReduction;
} bond_order_data;
typedef struct {
int nbr;
int sym_index;
int dbond_index;
ivec rel_box;
// rvec ext_factor;
double d;
rvec dvec;
bond_order_data bo_data;
} bond_data;
typedef struct {
int j;
double val;
} sparse_matrix_entry;
typedef struct {
int cap, n, m;
int *start, *end;
sparse_matrix_entry *entries;
} sparse_matrix;
typedef struct {
int num_far;
int H, Htop;
int hbonds, num_hbonds;
int bonds, num_bonds;
int num_3body;
int gcell_atoms;
} reallocate_data;
typedef struct
{
int allocated;
/* communication storage */
double *tmp_dbl[REAX_MAX_NBRS];
rvec *tmp_rvec[REAX_MAX_NBRS];
rvec2 *tmp_rvec2[REAX_MAX_NBRS];
int *within_bond_box;
/* bond order related storage */
double *total_bond_order;
double *Deltap, *Deltap_boc;
double *Delta, *Delta_lp, *Delta_lp_temp, *Delta_e, *Delta_boc, *Delta_val;
double *dDelta_lp, *dDelta_lp_temp;
double *nlp, *nlp_temp, *Clp, *vlpex;
rvec *dDeltap_self;
int *bond_mark, *done_after;
/* QEq storage */
sparse_matrix *H, *L, *U;
double *Hdia_inv, *b_s, *b_t, *b_prc, *b_prm, *s, *t;
double *droptol;
rvec2 *b, *x;
/* GMRES storage */
double *y, *z, *g;
double *hc, *hs;
double **h, **v;
/* CG storage */
double *r, *d, *q, *p;
rvec2 *r2, *d2, *q2, *p2;
/* Taper */
double Tap[8]; //Tap7, Tap6, Tap5, Tap4, Tap3, Tap2, Tap1, Tap0;
/* storage for analysis */
int *mark, *old_mark;
rvec *x_old;
/* storage space for bond restrictions */
int *restricted;
int **restricted_list;
/* integrator */
rvec *v_const;
/* force calculations */
double *CdDelta; // coefficient of dDelta
rvec *f;
/* omp */
rvec *forceReduction;
rvec *my_ext_pressReduction;
double *CdDeltaReduction;
int *valence_angle_atom_myoffset;
reallocate_data realloc;
} storage;
typedef union
{
void *v;
three_body_interaction_data *three_body_list;
bond_data *bond_list;
dbond_data *dbo_list;
dDelta_data *dDelta_list;
far_neighbor_data *far_nbr_list;
hbond_data *hbond_list;
} list_type;
struct _reax_list
{
int allocated;
int n;
int num_intrs;
int *index;
int *end_index;
int type;
list_type select;
};
typedef _reax_list reax_list;
typedef struct
{
FILE *strj;
int trj_offset;
int atom_line_len;
int bond_line_len;
int angle_line_len;
int write_atoms;
int write_bonds;
int write_angles;
char *line;
int buffer_len;
char *buffer;
FILE *out;
FILE *pot;
FILE *log;
FILE *mol, *ign;
FILE *dpl;
FILE *drft;
FILE *pdb;
FILE *prs;
int write_steps;
int traj_compress;
int traj_method;
char traj_title[81];
int atom_info;
int bond_info;
int angle_info;
int restart_format;
int restart_freq;
int debug_level;
int energy_update_freq;
} output_controls;
typedef struct
{
int atom_count;
int atom_list[REAX_MAX_MOLECULE_SIZE];
int mtypes[REAX_MAX_ATOM_TYPES];
} molecule;
struct LR_data
{
double H;
double e_vdW, CEvd;
double e_ele, CEclmb;
void operator = (const LR_data& rhs) {
H = rhs.H;
e_vdW = rhs.e_vdW;
CEvd = rhs.CEvd;
e_ele = rhs.e_ele;
CEclmb = rhs.CEclmb;
}
void operator = (const LR_data& rhs) volatile {
H = rhs.H;
e_vdW = rhs.e_vdW;
CEvd = rhs.CEvd;
e_ele = rhs.e_ele;
CEclmb = rhs.CEclmb;
}
};
struct cubic_spline_coef
{
double a, b, c, d;
void operator = (const cubic_spline_coef& rhs) {
a = rhs.a;
b = rhs.b;
c = rhs.c;
d = rhs.d;
}
void operator = (const cubic_spline_coef& rhs) volatile {
a = rhs.a;
b = rhs.b;
c = rhs.c;
d = rhs.d;
}
};
typedef struct
{
double xmin, xmax;
int n;
double dx, inv_dx;
double a;
double m;
double c;
LR_data *y;
cubic_spline_coef *H;
cubic_spline_coef *vdW, *CEvd;
cubic_spline_coef *ele, *CEclmb;
} LR_lookup_table;
extern LR_lookup_table **LR;
/* function pointer defs */
typedef void (*evolve_function)(reax_system*, control_params*,
simulation_data*, storage*, reax_list**,
output_controls*, mpi_datatypes* );
typedef void (*interaction_function) (reax_system*, control_params*,
simulation_data*, storage*,
reax_list**, output_controls*);
typedef void (*print_interaction)(reax_system*, control_params*,
simulation_data*, storage*,
reax_list**, output_controls*);
typedef double (*lookup_function)(double);
typedef void (*message_sorter) (reax_system*, int, int, int, mpi_out_data*);
typedef void (*unpacker) ( reax_system*, int, void*, int, neighbor_proc*, int );
typedef void (*dist_packer) (void*, mpi_out_data*);
typedef void (*coll_unpacker) (void*, void*, mpi_out_data*);
#endif

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