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Kurt A. O'Hearn authoredKurt A. O'Hearn authored
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mytypes.h 20.77 KiB
/*----------------------------------------------------------------------
SerialReax - Reax Force Field Simulator
Copyright (2010) Purdue University
Hasan Metin Aktulga, haktulga@cs.purdue.edu
Joseph Fogarty, jcfogart@mail.usf.edu
Sagar Pandit, pandit@usf.edu
Ananth Y Grama, ayg@cs.purdue.edu
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 __MYTYPES_H_
#define __MYTYPES_H_
#if (defined(HAVE_CONFIG_H) && !defined(__CONFIG_H_))
#define __CONFIG_H_
#include "config.h"
#endif
#include "math.h"
#include "random.h"
#include "stdio.h"
#include "stdlib.h"
#include "string.h"
#include "sys/time.h"
#include "time.h"
#include "zlib.h"
#ifdef _OPENMP
#include <omp.h>
#endif
//#define DEBUG_FOCUS
//#define TEST_FORCES
//#define TEST_ENERGY
#define REORDER_ATOMS // turns on nbrgen opt by re-ordering atoms
//#define LGJ
#define SUCCESS 1
#define FAILURE 0
#define TRUE 1
#define FALSE 0
#define EXP exp
#define SQRT sqrt
#define POW pow
#define ACOS acos
#define COS cos
#define SIN sin
#define TAN tan
#define FABS fabs
#define FMOD fmod
#define SQR(x) ((x)*(x))
#define CUBE(x) ((x)*(x)*(x))
#define DEG2RAD(a) ((a)*PI/180.0)
#define RAD2DEG(a) ((a)*180.0/PI)
#define MAX( x, y ) (((x) > (y)) ? (x) : (y))
#define MIN( x, y ) (((x) < (y)) ? (x) : (y))
/* NaN IEEE 754 representation for C99 in math.h
* Note: function choice must match REAL typedef below */
#ifdef NAN
#define IS_NAN_REAL(a) (isnan(a))
#else
#warn "No support for NaN"
#define NAN_REAL(a) (0)
#endif
#define PI 3.14159265
#define C_ele 332.06371
//#define K_B 503.398008 // kcal/mol/K
#define K_B 0.831687 // amu A^2 / ps^2 / K
#define F_CONV (1e6 / 48.88821291 / 48.88821291) // --> amu A / ps^2
#define E_CONV 0.002391 // amu A^2 / ps^2 --> kcal/mol
#define EV_to_KCALpMOL 14.400000 // ElectronVolt --> KCAL per MOLe
#define KCALpMOL_to_EV 23.060549 // 23.020000//KCAL per MOLe --> ElectronVolt
#define ECxA_to_DEBYE 4.803204 // elem. charge * angstrom -> debye conv
#define CAL_to_JOULES 4.184000 // CALories --> JOULES
#define JOULES_to_CAL (1/4.184000) // JOULES --> CALories
#define AMU_to_GRAM 1.6605e-24
#define ANG_to_CM 1.0e-8
#define AVOGNR 6.0221367e23
#define P_CONV (1.0e-24 * AVOGNR * JOULES_to_CAL)
#define MAX_STR 1024
#define MAX_LINE 1024
#define MAX_TOKENS 1024
#define MAX_TOKEN_LEN 1024
#define MAX_ATOM_ID 100000
#define MAX_RESTRICT 15
#define MAX_MOLECULE_SIZE 20
#define MAX_ATOM_TYPES 25
#define MAX_GRID 50
#define MAX_3BODY_PARAM 5
#define MAX_4BODY_PARAM 5
#define NO_OF_INTERACTIONS 10
#define MAX_dV 1.01
#define MIN_dV 0.99
#define MAX_dT 4.00
#define MIN_dT 0.00
#define ZERO 0.000000000000000e+00
#define ALMOST_ZERO 1e-10
#define NEG_INF -1e10
#define NO_BOND 1e-3
#define HB_THRESHOLD 1e-2
#define MAX_BONDS 40
#define MIN_BONDS 15
#define MIN_HBONDS 50
#define SAFE_HBONDS 1.4
#define MIN_GCELL_POPL 50
#define SAFE_ZONE 1.2
#define DANGER_ZONE 0.95
#define LOOSE_ZONE 0.75
typedef double real;
typedef real rvec[3];
typedef int ivec[3];
typedef real rtensor[3][3];
/* config params */
enum ensemble
{
NVE = 0, NVT = 1, NPT = 2, sNPT = 3, iNPT = 4, ensNR = 5, bNVT = 6,
};
enum interaction_list_offets
{
FAR_NBRS = 0, NEAR_NBRS = 1, THREE_BODIES = 2, BONDS = 3, OLD_BONDS = 4,
HBONDS = 5, DBO = 6, DDELTA = 7, LIST_N = 8,
};
enum interaction_type
{
TYP_VOID = 0, TYP_THREE_BODY = 1, TYP_BOND = 2, TYP_HBOND = 3, TYP_DBO = 4,
TYP_DDELTA = 5, TYP_FAR_NEIGHBOR = 6, TYP_NEAR_NEIGHBOR = 7, TYP_N = 8,
};
enum errors
{
FILE_NOT_FOUND = -10,
UNKNOWN_ATOM_TYPE = -11,
CANNOT_OPEN_FILE = -12,
CANNOT_INITIALIZE = -13,
INSUFFICIENT_MEMORY = -14,
UNKNOWN_OPTION = -15,
INVALID_INPUT = -16,
INVALID_GEO = -17,
NUMERIC_BREAKDOWN = -18,
RUNTIME_ERROR = -19,
};
enum atoms
{
C_ATOM = 0, H_ATOM = 1, O_ATOM = 2, N_ATOM = 3,
S_ATOM = 4, SI_ATOM = 5, GE_ATOM = 6, X_ATOM = 7,
};
enum molecule_type
{
UNKNOWN = 0, WATER = 1,
};
enum molecular_analysis_type
{
NO_ANALYSIS = 0, FRAGMENTS = 1, REACTIONS = 2, NUM_ANALYSIS = 3,
};
enum restart_format
{
WRITE_ASCII = 0, WRITE_BINARY = 1, RF_N = 2,
};
enum geo_formats
{
CUSTOM = 0, PDB = 1, BGF = 2, ASCII_RESTART = 3, BINARY_RESTART = 4, GF_N = 5,
};
enum charge_method
{
QEQ_CM = 0, EEM_CM = 1, ACKS2_CM = 2,
};
enum solver
{
GMRES_S = 0, GMRES_H_S = 1, CG_S = 2, SDM_S = 3,
};
enum pre_comp
{
DIAG_PC = 0, ICHOLT_PC = 1, ILU_PAR_PC = 2, ILUT_PAR_PC = 3, ILU_SUPERLU_MT_PC = 4,
};
enum pre_app
{ NONE_PA = 0, TRI_SOLVE_PA = 1, TRI_SOLVE_LEVEL_SCHED_PA = 2, TRI_SOLVE_GC_PA = 3, JACOBI_ITER_PA = 4,
};
/* Force field 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] = N/A
l[12] = N/A
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] = ACKS2 bond softness
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; /* Determines whether this type of atom participates in H_bonds.
It is 1 for donor H, 2 for acceptors (O,S,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;
real b_s_acks2; /* bond softness for ACKS2 */
/* Line four in the field file */
real p_ovun2;
real p_val3;
real valency_val;
real p_val5;
real rcore2;
real ecore2;
real acore2;
} 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;
/* 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[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[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 type; /* Type of this atom */
char name[8];
rvec x; // position
rvec v; // velocity
rvec f; // force
real q; /* Charge on the atom */
} reax_atom;
typedef struct
{
real volume;
rvec box_norms;
rvec side_prop;
rvec nbr_box_press[27];
// rvec lower_end;
rtensor box, box_inv, old_box;
rtensor trans, trans_inv;
rtensor g;
} simulation_box;
typedef struct
{
int max_atoms;
int max_nbrs;
int total;
real cell_size;
ivec spread;
ivec ncell;
rvec len;
rvec inv_len;
int**** atoms;
int*** top;
int*** mark;
int*** start;
int*** end;
ivec**** nbrs;
rvec**** nbrs_cp;
} grid;
typedef struct
{
/* number of atoms */
int N;
/* dimension of the N x N sparse charge method matrix H */
int N_cm;
/* atom info */
reax_atom *atoms;
/* atomic interaction parameters */
reax_interaction reaxprm;
/* simulation space (a.k.a. box) parameters */
simulation_box box;
/* grid structure used for binning atoms and tracking neighboring bins */
grid g;
} reax_system;
/* Simulation control parameters not related to the system */
typedef struct
{
char sim_name[MAX_STR];
char restart_from[MAX_STR];
int restart;
int random_vel;
int reposition_atoms;
/* ensemble values:
0 : NVE
1 : NVT (Nose-Hoover)
2 : NPT (Parrinello-Rehman-Nose-Hoover) Anisotropic
3 : sNPT (Parrinello-Rehman-Nose-Hoover) semiisotropic
4 : iNPT (Parrinello-Rehman-Nose-Hoover) isotropic */
int ensemble;
int nsteps;
int periodic_boundaries; int restrict_bonds;
int tabulate;
ivec periodic_images;
real dt;
int reneighbor;
real vlist_cut;
real nbr_cut;
real r_cut, r_sp_cut, r_low; // upper and lower taper
real bo_cut;
real thb_cut;
real hb_cut;
real Tap7, Tap6, Tap5, Tap4, Tap3, Tap2, Tap1, Tap0;
int max_far_nbrs;
real T_init, T_final, T;
real Tau_T;
int T_mode;
real T_rate, T_freq;
real Tau_PT;
rvec P, Tau_P;
int press_mode;
real compressibility;
int remove_CoM_vel;
int geo_format;
int dipole_anal;
int freq_dipole_anal;
int diffusion_coef;
int freq_diffusion_coef;
int restrict_type;
unsigned int charge_method;
unsigned int cm_solver_type;
real cm_q_net;
unsigned int cm_solver_max_iters;
unsigned int cm_solver_restart;
real cm_solver_q_err;
real cm_domain_sparsity;
unsigned int cm_domain_sparsify_enabled;
unsigned int cm_solver_pre_comp_type;
unsigned int cm_solver_pre_comp_refactor;
real cm_solver_pre_comp_droptol;
unsigned int cm_solver_pre_comp_sweeps;
unsigned int cm_solver_pre_app_type;
unsigned int cm_solver_pre_app_jacobi_iters;
int molec_anal;
int freq_molec_anal;
real bg_cut;
int num_ignored;
int ignore[MAX_ATOM_TYPES];
} 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 nbrs;
real init_forces;
real bonded;
real nonb;
real cm;
real cm_sort_mat_rows;
real cm_solver_pre_comp;
real cm_solver_pre_app;
int cm_solver_iters;
real cm_solver_spmv;
real cm_solver_vector_ops;
real cm_solver_orthog;
real cm_solver_tri_solve;
} reax_timing;
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 */
real E_Tot;
real E_Kin; /* Total kinetic energy */
real E_Pot;
real E_BE; /* 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 */
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;
rvec int_press;
rvec ext_press;
real kin_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;
// rvec ext_factor;
real d;
rvec dvec;
} near_neighbor_data;
typedef struct
{
int nbr;
ivec rel_box;
// rvec ext_factor;
real d;
rvec dvec;
// real H; //, Tap, inv_dr3gamij_1, inv_dr3gamij_3;
} 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;
/* compressed row storage (crs) format
* See, e.g.,
* http://netlib.org/linalg/html_templates/node91.html#SECTION00931100000000000000
*
* m: number of nonzeros (NNZ) ALLOCATED
* n: number of rows
* start: row pointer (last element contains ACTUAL NNZ)
* j: column index for corresponding matrix entry
* val: matrix entry
* */
typedef struct
{
unsigned int n, m;
unsigned int *start;
unsigned int *j;
real *val;
} sparse_matrix;
typedef struct
{
int num_far;
int Htop;
int hbonds;
int num_hbonds;
int bonds;
int num_bonds;
int num_3body;
int gcell_atoms;
} reallocate_data;
typedef struct
{
/* bond order related storage */
real *total_bond_order;
real *Deltap, *Deltap_boc;
real *Delta, *Delta_lp, *Delta_lp_temp, *Delta_e, *Delta_boc;
real *dDelta_lp, *dDelta_lp_temp;
real *nlp, *nlp_temp, *Clp, *vlpex;
rvec *dDeltap_self;
/* charge method storage */
sparse_matrix *H, *H_sp, *L, *U;
/* EEM-specific */
sparse_matrix *H_EEM, *L_EEM, *U_EEM;
/* ACKS2-specific */
sparse_matrix *H_ACKS2_1, *H_ACKS2_2, *L_ACKS2_1, *L_ACKS2_2, *U_ACKS2_1, *U_ACKS2_2;
real *droptol;
real *w;
real *Hdia_inv;
real *b, *b_s, *b_t, *b_prc, *b_prm;
real **s, **t;
real *s_t; //, *s_old, *t_old, *s_oldest, *t_oldest;
/* GMRES related storage */
real *y, *z, *g;
real *hc, *hs;
real **h, **rn, **v;
/* CG related storage */
real *r, *d, *q, *p;
int s_dims, t_dims;
int num_H;
int *hbond_index; // for hydrogen bonds
rvec *v_const, *f_old, *a; // used in integrators
real *CdDelta; // coefficient of dDelta for force calculations
int *mark, *old_mark; // storage for analysis
rvec *x_old;
/* storage space for bond restrictions */
int *map_serials;
int *orig_id;
int *restricted;
int **restricted_list;
reallocate_data realloc;
#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 *dDelta; /* Calculated on the fly in bond_orders.c */
#endif
} static_storage;
/* interaction lists */typedef struct
{
int n;
int num_intrs;
int *index;
int *end_index;
int type;
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;
near_neighbor_data *near_nbr_list;
hbond_data *hbond_list;
} select;
} list;
typedef struct
{
FILE *trj;
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_format;
char traj_title[81];
int atom_format;
int bond_info;
int angle_info;
int restart_format;
int restart_freq;
int debug_level;
int energy_update_freq;
// trajectory output functions
int (* write_header)( reax_system*, control_params*, static_storage*, void* );
int (* append_traj_frame)(reax_system*, control_params*,
simulation_data*, static_storage*, list **, void* );
int (* write)( FILE *, const char *, ... );
#ifdef TEST_ENERGY
FILE *ebond;
FILE *elp, *eov, *eun;
FILE *eval, *epen, *ecoa;
FILE *ehb;
FILE *etor, *econ;
FILE *evdw, *ecou;
#endif
FILE *ftot;
#ifdef TEST_FORCES
FILE *fbo, *fdbo;
FILE *fbond;
FILE *flp, *fatom;
FILE *f3body;
FILE *fhb;
FILE *f4body;
FILE *fnonb; FILE *ftot2;
#endif
} output_controls;
typedef struct
{
int atom_count;
int atom_list[MAX_MOLECULE_SIZE];
int mtypes[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;
real *y;
} lookup_table;
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;
typedef void (*interaction_function)(reax_system*, control_params*,
simulation_data*, static_storage*,
list**, output_controls*);
interaction_function Interaction_Functions[NO_OF_INTERACTIONS];
typedef void (*evolve_function)(reax_system*, control_params*,
simulation_data*, static_storage*,
list**, output_controls*);
typedef real (*lookup_function)(real);
lookup_table Exp, Sqrt, Cube_Root, Four_Third_Root, Cos, Sin, ACos;
LR_lookup_table **LR;
typedef void (*get_far_neighbors_function)(rvec, rvec, simulation_box*,
control_params*, far_neighbor_data*,
int*);
#endif