reaxc_types.h
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Created: Thu, Jun 6, 15:11

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 "ctype.h"
	#include "math.h"
	#include "mpi.h"
	#include "stdio.h"
	#include "stdlib.h"
	#include "string.h"
	#include "sys/time.h"
	#include "time.h"

	/*********** SOME DEFS - crucial for reax_types.h *******/

	//#define PURE_REAX
	#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 real;
	typedef real rvec[3];
	typedef real rtensor[3][3];
	typedef real rvec2[2];
	typedef real rvec4[4];


	typedef struct {
	int step, bigN;
	real T, xi, v_xi, v_xi_old, G_xi;
	rtensor box;
	} restart_header;

	typedef struct {
	int orig_id, type;
	char name[8];
	rvec x, v;
	} restart_atom;

	typedef struct
	{
	int orig_id;
	int imprt_id;
	int type;
	int num_bonds;
	int num_hbonds;
	//int pad; // pad to 8-byte address boundary
	char name[8];
	rvec x; // position
	rvec v; // velocity
	rvec f_old; // old force
	rvec4 s, t; // for calculating q
	} mpi_atom;


	typedef struct
	{
	int orig_id;
	int imprt_id;
	int type;
	int num_bonds;
	int num_hbonds;
	//int pad;
	rvec x; // position
	} boundary_atom;


	typedef struct
	{
	//int ncells;
	//int *cnt_by_gcell;

	int cnt;
	//int *block;
	int *index;
	//MPI_Datatype out_dtype;
	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_Request send_req1[REAX_MAX_NBRS];
	//MPI_Request send_req2[REAX_MAX_NBRS];
	//MPI_Status send_stat1[REAX_MAX_NBRS];
	//MPI_Status send_stat2[REAX_MAX_NBRS];
	//MPI_Status recv_stat1[REAX_MAX_NBRS];
	//MPI_Status recv_stat2[REAX_MAX_NBRS];

	mpi_out_data out_buffers[REAX_MAX_NBRS];
	void *in1_buffer;
	void *in2_buffer;
	} mpi_datatypes;


	/* Global params mapping */
	/*
	l[0] = p_boc1
	l[1] = p_boc2
	l[2] = p_coa2
	l[3] = N/A
	l[4] = N/A
	l[5] = N/A
	l[6] = p_ovun6
	l[7] = N/A
	l[8] = p_ovun7
	l[9] = p_ovun8
	l[10] = N/A
	l[11] = swa
	l[12] = swb
	l[13] = N/A
	l[14] = p_val6
	l[15] = p_lp1
	l[16] = p_val9
	l[17] = p_val10
	l[18] = N/A
	l[19] = p_pen2
	l[20] = p_pen3
	l[21] = p_pen4
	l[22] = N/A
	l[23] = p_tor2
	l[24] = p_tor3
	l[25] = p_tor4
	l[26] = N/A
	l[27] = p_cot2
	l[28] = p_vdW1
	l[29] = v_par30
	l[30] = p_coa4
	l[31] = p_ovun4
	l[32] = p_ovun3
	l[33] = p_val8
	l[34] = N/A
	l[35] = N/A
	l[36] = N/A
	l[37] = version number
	l[38] = p_coa3
	*/

	typedef struct
	{
	int n_global;
	real* l;
	int vdw_type;
	} global_parameters;



	typedef struct
	{
	/* Line one in field file */
	char name[15]; // Two character atom name

	real r_s;
	real valency; // Valency of the atom
	real mass; // Mass of atom
	real r_vdw;
	real epsilon;
	real gamma;
	real r_pi;
	real valency_e;
	real nlp_opt;

	/* Line two in field file */
	real alpha;
	real gamma_w;
	real valency_boc;
	real p_ovun5;
	real chi;
	real eta;
	int p_hbond; // 1 for H, 2 for hbonding atoms (O,S,P,N), 0 for others

	/* Line three in field file */
	real r_pi_pi;
	real p_lp2;
	real b_o_131;
	real b_o_132;
	real b_o_133;

	/* Line four in the field file */
	real p_ovun2;
	real p_val3;
	real valency_val;
	real p_val5;
	real rcore2;
	real ecore2;
	real acore2;

	/* Line five in the ffield file, only for lgvdw yes */
	real lgcij;
	real lgre;

	} single_body_parameters;



	/* Two Body Parameters */
	typedef struct {
	/* Bond Order parameters */
	real p_bo1,p_bo2,p_bo3,p_bo4,p_bo5,p_bo6;
	real r_s, r_p, r_pp; // r_o distances in BO formula
	real p_boc3, p_boc4, p_boc5;

	/* Bond Energy parameters */
	real p_be1, p_be2;
	real De_s, De_p, De_pp;

	/* Over/Under coordination parameters */
	real p_ovun1;

	/* Van der Waal interaction parameters */
	real D;
	real alpha;
	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.

	real v13cor, ovc;
	} two_body_parameters;



	/* 3-body parameters */
	typedef struct {
	/* valence angle */
	real theta_00;
	real p_val1, p_val2, p_val4, p_val7;

	/* penalty */
	real p_pen1;

	/* 3-body conjugation */
	real 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{
	real r0_hb, p_hb1, p_hb2, p_hb3;
	} hbond_parameters;



	/* 4-body parameters */
	typedef struct {
	real V1, V2, V3;

	/* torsion angle */
	real p_tor1;

	/* 4-body conjugation */
	real 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;



	typedef struct
	{
	int orig_id;
	int imprt_id;
	int type;
	char name[8];

	rvec x; // position
	rvec v; // velocity
	rvec f; // force
	rvec f_old;

	real 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
	} reax_atom;



	typedef struct
	{
	real V;
	rvec min, max, box_norms;

	rtensor box, box_inv;
	rtensor trans, trans_inv;
	rtensor g;
	} simulation_box;



	struct grid_cell
	{
	real 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;

	real 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
	{
	real ghost_nonb;
	real ghost_hbond;
	real ghost_bond;
	real ghost_cutoff;
	} boundary_cutoff;

	using LAMMPS_NS::Pair;

	typedef struct
	{
	reax_interaction reax_param;

	int n, N, bigN, 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;

	} reax_system;



	/* system control parameters */
	typedef struct
	{
	char sim_name[REAX_MAX_STR];
	int nprocs;
	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;
	real dt;
	int geo_format;
	int restart;

	int restrict_bonds;
	int remove_CoM_vel;
	int random_vel;
	int reposition_atoms;

	int reneighbor;
	real vlist_cut;
	real bond_cut;
	real nonb_cut, nonb_low;
	real hbond_cut;
	real user_ghost_cut;

	real bg_cut;
	real bo_cut;
	real thb_cut;

	int tabulate;

	int qeq_freq;
	real q_err;
	int refactor;
	real droptol;

	real T_init, T_final, T;
	real Tau_T;
	int T_mode;
	real T_rate, T_freq;

	int virial;
	rvec P, Tau_P, Tau_PT;
	int press_mode;
	real 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;

	} control_params;


	typedef struct
	{
	real T;
	real xi;
	real v_xi;
	real v_xi_old;
	real G_xi;

	} thermostat;


	typedef struct
	{
	real P;
	real eps;
	real v_eps;
	real v_eps_old;
	real a_eps;

	} isotropic_barostat;


	typedef struct
	{
	rtensor P;
	real P_scalar;

	real eps;
	real v_eps;
	real v_eps_old;
	real a_eps;

	rtensor h0;
	rtensor v_g0;
	rtensor v_g0_old;
	rtensor a_g0;

	} flexible_barostat;


	typedef struct
	{
	real start;
	real end;
	real elapsed;

	real total;
	real comm;
	real nbrs;
	real init_forces;
	real bonded;
	real nonb;
	real qEq;
	int s_matvecs;
	int t_matvecs;
	} reax_timing;


	typedef struct
	{
	real e_tot;
	real e_kin; // Total kinetic energy
	real e_pot;

	real e_bond; // Total bond energy
	real e_ov; // Total over coordination
	real e_un; // Total under coordination energy
	real e_lp; // Total under coordination energy
	real e_ang; // Total valance angle energy
	real e_pen; // Total penalty energy
	real e_coa; // Total three body conjgation energy
	real e_hb; // Total Hydrogen bond energy
	real e_tor; // Total torsional energy
	real e_con; // Total four body conjugation energy
	real e_vdW; // Total van der Waals energy
	real e_ele; // Total electrostatics energy
	real e_pol; // Polarization energy
	} energy_data;

	typedef struct
	{
	int step;
	int prev_steps;
	real time;

	real M; // Total Mass
	real 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
	real etran_cm; // Translational kinetic energy of CoM
	real erot_cm; // Rotational kinetic energy of CoM

	rtensor kinetic; // Kinetic energy tensor
	rtensor virial; // Hydrodynamic virial

	energy_data my_en;
	energy_data sys_en;

	real 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;
	real inv_W;

	real 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
	real theta, cos_theta;
	rvec dcos_di, dcos_dj, dcos_dk;
	} three_body_interaction_data;


	typedef struct {
	int nbr;
	ivec rel_box;
	real 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{
	real BO, BO_s, BO_pi, BO_pi2;
	real Cdbo, Cdbopi, Cdbopi2;
	real C1dbo, C2dbo, C3dbo;
	real C1dbopi, C2dbopi, C3dbopi, C4dbopi;
	real C1dbopi2, C2dbopi2, C3dbopi2, C4dbopi2;
	rvec dBOp, dln_BOp_s, dln_BOp_pi, dln_BOp_pi2;
	} bond_order_data;

	typedef struct {
	int nbr;
	int sym_index;
	int dbond_index;
	ivec rel_box;
	// rvec ext_factor;
	real d;
	rvec dvec;
	bond_order_data bo_data;
	} bond_data;


	typedef struct {
	int j;
	real 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 */
	real *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 */
	real *total_bond_order;
	real Deltap, Deltap_boc;
	real Delta, Delta_lp, Delta_lp_temp, Delta_e, Delta_boc, Delta_val;
	real dDelta_lp, dDelta_lp_temp;
	real nlp, nlp_temp, Clp, vlpex;
	rvec *dDeltap_self;
	int bond_mark, done_after;

	/* QEq storage */
	sparse_matrix H, L, *U;
	real Hdia_inv, b_s, b_t, b_prc, b_prm, s, *t;
	real *droptol;
	rvec2 b, x;

	/* GMRES storage */
	real y, z, *g;
	real hc, hs;
	real h, v;
	/* CG storage */
	real r, d, q, p;
	rvec2 r2, d2, q2, p2;
	/* Taper */
	real 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 */
	real *CdDelta; // coefficient of dDelta
	rvec *f;
	#ifdef TEST_FORCES
	rvec *f_ele;
	rvec *f_vdw;
	rvec *f_bo;
	rvec *f_be;
	rvec *f_lp;
	rvec *f_ov;
	rvec *f_un;
	rvec *f_ang;
	rvec *f_coa;
	rvec *f_pen;
	rvec *f_hb;
	rvec *f_tor;
	rvec *f_con;
	rvec *f_tot;
	rvec *dDelta; // calculated on the fly in bond_orders.c together with bo'

	int *rcounts;
	int *displs;
	int *id_all;
	rvec *f_all;
	#endif

	reallocate_data realloc;
	//int *num_bonds;
	/* hydrogen bonds */
	//int num_H, Hcap;
	//int *Hindex;
	//int *num_hbonds;
	//int *hash;
	//int *rev_hash;
	} 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;


	typedef struct
	{
	int allocated;

	int n;
	int num_intrs;

	int *index;
	int *end_index;

	int type;
	list_type select;
	} reax_list;


	typedef struct
	{
	#if defined(PURE_REAX)
	MPI_File trj;
	#endif
	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;

	#ifdef TEST_ENERGY
	FILE *ebond;
	FILE elp, eov, *eun;
	FILE eval, epen, *ecoa;
	FILE *ehb;
	FILE etor, econ;
	FILE evdw, ecou;
	#endif

	#ifdef TEST_FORCES
	FILE fbo, fdbo;
	FILE *fbond;
	FILE flp, fov, *fun;
	FILE fang, fcoa, *fpen;
	FILE *fhb;
	FILE ftor, fcon;
	FILE fvdw, fele;
	FILE ftot, fcomp;
	#endif

	#if defined(TEST_ENERGY) \|\| defined(TEST_FORCES)
	FILE *flist; // far neighbor list
	FILE *blist; // bond list
	FILE *nlist; // near neighbor list
	#endif
	} output_controls;


	typedef struct
	{
	int atom_count;
	int atom_list[REAX_MAX_MOLECULE_SIZE];
	int mtypes[REAX_MAX_ATOM_TYPES];
	} molecule;


	typedef struct
	{
	real H;
	real e_vdW, CEvd;
	real e_ele, CEclmb;
	} LR_data;


	typedef struct
	{
	real a, b, c, d;
	} cubic_spline_coef;



	typedef struct
	{
	real xmin, xmax;
	int n;
	real dx, inv_dx;
	real a;
	real m;
	real 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 );
	#if defined(PURE_REAX)
	evolve_function Evolve;
	#endif

	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 real (*lookup_function)(real);

	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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