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This commit is contained in:
Nils Berglund
2024-06-01 16:54:53 +02:00
committed by GitHub
parent f773d3940d
commit 008fbf4612
19 changed files with 5701 additions and 774 deletions
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47
global_ljones.c
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@@ -18,6 +18,7 @@
#define NMAXGROUPS 50 /* max number of groups of segments */
#define NMAXCOLLISIONS 200000 /* max number of collisions */
#define NMAXPARTNERS 30 /* max number of partners in molecule */
#define NMAXPARTNERMOLECULES 10 /* max number of partners of a molecule */
#define C_SQUARE 0 /* square grid of circles */
#define C_HEX 1 /* hexagonal/triangular grid of circles */
@@ -48,6 +49,8 @@
#define O_CIRCLE 4 /* one circle at the origin */
#define O_FOUR_CIRCLES 5 /* four circles */
#define O_HEX 6 /* hexagonal lattice */
#define O_SIDES 7 /* grid along the sides of the simulation rectangle */
#define O_SIDES_B 71 /* finer grid along the sides of the simulation rectangle */
/* pattern of additional repelling segments */
#define S_RECTANGLE 0 /* segments forming a rectangle */
@@ -101,6 +104,10 @@
#define I_VICSEK_SPEED 10 /* Vicsek-type interaction with speed adjustment */
#define I_VICSEK_SHARK 11 /* Vicsek-type interaction with speed adjustment, and one shark */
#define I_COULOMB_LJ 12 /* Coulomb force regularised by Lennard-Jones repulsion */
#define I_COULOMB_PENTA 13 /* Lennard-Jones force with or without pentagonal symmetry depending on charge */
#define I_COULOMB_IMAGINARY 14 /* Coulomb interaction with "imaginary charge" */
#define I_DNA_CHARGED 15 /* Coulomb-type interaction between end points of DNA nucleotides */
#define I_DNA_CHARGED_B 151 /* stronger Coulomb-type interaction between end points of DNA nucleotides */
/* Boundary conditions */
@@ -144,6 +151,8 @@
#define TS_COSINE 4 /* periodic time dependence, cosine */
#define TS_EXPCOS 5 /* periodic time dependence, exponential of cosine */
#define TS_ASYM_EXPCOS 6 /* periodic time dependence, asymmetric exponential of cosine */
#define TS_ATAN 7 /* atan approaching asymptotic value */
#define TS_TANH 8 /* tanh approaching asymptotic value */
/* Gravity schedules */
@@ -191,6 +200,14 @@
#define CHEM_2H2O_H3O_OH 21 /* 2 H2O <-> H3O+ + OH- */
#define CHEM_AGGREGATION 22 /* agregation of molecules coming close */
#define CHEM_AGGREGATION_CHARGE 23 /* agregation of charged molecules coming close */
#define CHEM_AGGREGATION_NNEIGH 24 /* agregation of molecules with limitation on neighbours */
#define CHEM_DNA 25 /* aggregation of DNA molecules */
#define CHEM_DNA_ALT 251 /* aggregation of DNA molecules with constraints on connections */
#define CHEM_DNA_DOUBLE 252 /* aggregation of DNA molecules with different ends */
#define CHEM_DNA_DSPLIT 253 /* aggregation/splitting of DNA molecules with different ends */
#define CHEM_DNA_BASE_SPLIT 254 /* aggregation/splitting of DNA molecules when base pairs don't match */
#define CHEM_DNA_ENZYME 255 /* aggregation/splitting of DNA molecules in presence of enzymes */
#define CHEM_DNA_ENZYME_REPAIR 256 /* aggregation/splitting of DNA molecules in presence of enzymes and additional repairing of bad connections */
/* Initial conditions for chemical reactions */
@@ -206,6 +223,8 @@
#define IC_SIGNX 7 /* type 1 or 2 depending on sign of x */
#define IC_TWOROCKETS 8 /* type 1 or 2 depending on rocket position */
#define IC_TWOROCKETS_TWOFUELS 9 /* type 1 and 2 or 1 and 3 depending on rocket */
#define IC_DNA_POLYMERASE 10 /* initial condition for DNA polymerase */
#define IC_DNA_POLYMERASE_REC 11 /* initial condition for DNA polymerase with recombination */
/* Initial conditions for option TWO_TYPES */
@@ -259,10 +278,15 @@
#define POLY_WATER 2 /* star-shaped with a 120° separation between anions */
#define POLY_SOAP 3 /* polymers with all-to-all coupling and polar end */
#define POLY_SOAP_B 4 /* polymers with pairwise coupling and polar end */
#define POLY_SOAP_N 41 /* polymers with pairwise coupling and neutral polar end */
#define POLY_SOAP_NMIX 42 /* polymers mixing neutral polar and neutral end */
#define POLY_PLUSMINUS 5 /* polymers with ends of opposite charge */
#define POLY_HYDRA 6 /* star-shaped with longer arms */
#define POLY_HYDRA_RIGID 61 /* star-shaped with longer arms and rigid first ring */
// #define POLY_GLUE 99 /* dummy value for option CHEM_AGGREGATION */
#define POLY_DNA 7 /* simplified model for DNA */
#define POLY_DNA_ALT 71 /* simplified model for DNA with different short ends */
#define POLY_DNA_DOUBLE 72 /* simplified model for DNA with double ends for rigidity */
#define POLY_DNA_FLEX 73 /* simplified model for DNA with less backbone rigidity (beta) */
/* Background color schemes */
@@ -342,8 +366,15 @@ typedef struct
short int npartners; /* number of partner particles */
double partner_eqd[NMAXPARTNERS]; /* equilibrium distances between partners */
int p0, p1; /* numbers of two first partners (for P_MOL_ANGLE color scheme) */
// short int mol_angle; /* for color scheme P_MOL_ANGLE */
int cluster; /* number of cluster */
short int tested, cactive; /* for cluster search */
int molecule; /* number of molecule */
short int tested, cactive; /* for cluster search */
short int coulomb; /* has value 1 if DNA-Coulomb interaction is attractive */
short int added; /* has value 1 if particle has been added */
short int reactive; /* has value 1 if particle can react */
short int paired; /* has value 1 if belongs to base-paired molecule */
int partner_molecule; /* number of partner molecule */
} t_particle;
typedef struct
@@ -434,6 +465,15 @@ typedef struct
int color; /* color hue in case of different collisions */
} t_collision;
typedef struct
{
int nparticles; /* number of particles */
int particle[NPARTNERS+1]; /* list of particles */
int npartners; /* number of partner molecules */
int partner[NMAXPARTNERMOLECULES]; /* list of partner molecules */
int connection_type[NMAXPARTNERMOLECULES]; /* types of particles in connection */
short int added; /* has value 1 if molecule has been added */
} t_molecule;
typedef struct
{
@@ -456,5 +496,6 @@ typedef struct
int ncircles, nobstacles, nsegments, ngroups = 1, counter = 0;
int frame_time = 0, ncircles, nobstacles, nsegments, ngroups = 1, counter = 0, nmolecules = 0;
FILE *lj_log;