From 06912ca45b46de412570a4bd5b5484aa9e8d6e6b Mon Sep 17 00:00:00 2001 From: hackbard Date: Tue, 21 Nov 2006 17:35:39 +0000 Subject: [PATCH] more updates --- moldyn.c | 122 +++++++++++++++++++++++++++++++++++++++++++++---------- moldyn.h | 103 +++++++++++++++++++++++----------------------- 2 files changed, 154 insertions(+), 71 deletions(-) diff --git a/moldyn.c b/moldyn.c index f92ce55..57f76c4 100644 --- a/moldyn.c +++ b/moldyn.c @@ -58,6 +58,7 @@ int moldyn_parse_argv(t_moldyn *moldyn,int argc,char **argv) { int i; t_ho_params hop; t_lj_params ljp; + t_tersoff_params tp; double s,e; memset(moldyn,0,sizeof(t_moldyn)); @@ -81,10 +82,6 @@ int moldyn_parse_argv(t_moldyn *moldyn,int argc,char **argv) { moldyn->mwrite=atoi(argv[++i]); strncpy(moldyn->mfb,argv[++i],64); break; - case 'D': - moldyn->dwrite=atoi(argv[++i]); - strncpy(moldyn->dfb,argv[++i],64); - break; case 'S': moldyn->swrite=atoi(argv[++i]); strncpy(moldyn->sfb,argv[++i],64); @@ -187,16 +184,6 @@ int moldyn_log_init(t_moldyn *moldyn) { if(moldyn->swrite) moldyn->lvstat|=MOLDYN_LVSTAT_SAVE; - if(moldyn->dwrite) { - moldyn->dfd=open(moldyn->dfb,O_WRONLY|O_CREAT|O_TRUNC); - if(moldyn->dfd<0) { - perror("[moldyn] dfd open"); - return moldyn->dfd; - } - write(moldyn->dfd,moldyn,sizeof(t_moldyn)); - moldyn->lvstat|=MOLDYN_LVSTAT_DUMP; - } - if((moldyn->vwrite)&&(vis)) { moldyn->visual=vis; visual_init(vis,moldyn->vfb); @@ -544,6 +531,9 @@ int link_cell_neighbour_index(t_moldyn *moldyn,int i,int j,int k,t_list *cell) { } } + lc->dnlc=count2; + lc->countn=27; + return count2; } @@ -632,14 +622,9 @@ int moldyn_integrate(t_moldyn *moldyn) { write(fd,moldyn->atom, moldyn->count*sizeof(t_atom)); } + close(fd); } } - if(d) { - if(!(i%d)) - write(moldyn->dfd,moldyn->atom, - moldyn->count*sizeof(t_atom)); - - } if(v) { if(!(i%v)) { visual_atoms(moldyn->visual,i*moldyn->tau, @@ -687,7 +672,8 @@ printf("done\n"); /* forces depending on chosen potential */ printf("calc potential/force ...\n"); - moldyn->potential_force_function(moldyn); + potential_force_calc(moldyn); + //moldyn->potential_force_function(moldyn); printf("done\n"); for(i=0;idim.x/2)/lc->x,\ + (atom[i].r.y+moldyn->dim.y/2)/lc->y,\ + (atom[i].r.z+moldyn->dim.z/2)/lc->z,\ + nb_list); + + +int potential_force_calc(t_moldyn *moldyn) { + + int i,count; + t_atom *atom; + t_linkcell *lc; + t_list neighbour[27]; + t_list *this; + double u; + + count=moldyn->count; + atom=moldyn->atom; + lc=&(moldyn->lc); + + /* reset energy */ + u=0.0; + + for(i=0;istatus&MOLDYN_STAT_1BP) + moldyn->pf_func1b(moldyn,&(atom[i])); + + /* 2 body pair potential/force */ + if(moldyn->status&MOLDYN_STAT_2BP) { + + CREATE_CELL_LIST(neighbour); + + /* + * processing cell of atom i + * => no need to check for empty list + * (1 element at minimum) + */ + + this=&(neighbour[0]); + list_reset(this); + do { + btom=this->current->data; + if(btom!=&(atom[i])) + moldyn->pf_func2b(moldyn, + &(atom[i]),btom); + } while(list_next(this)!=L_NO_NEXT_ELEMENT); + + /* + * direct neighbour cells + * => no boundary condition check necessary + */ + for(j=0;jdnlc;j++) { + this=&(neighbour[j]); + list_reset(this); + if(this->start!=NULL) { + do { + btom=this->current->data; + moldyn->pf_func2b(moldyn, + &(atom[i]), + btom); + } while(list_next(this)!=\ + L_NO_NEXT_ELEMENT); + } + + /* + * neighbour cells due to periodic bc + * => check boundary conditions + */ + for(j=lc->dnlc;jcountn;j++) { + this=&(neighbour[j]); + list_reset(this); + if(this->start!=NULL) { + do { + btom=this->current->data; + moldyn->pf_func2b(moldyn, + &(atom[i]), + btom); + + } + + } + + return 0; +} + + /* harmonic oscillator potential and force */ int harmonic_oscillator(t_moldyn *moldyn) { diff --git a/moldyn.h b/moldyn.h index c6712ba..717388a 100644 --- a/moldyn.h +++ b/moldyn.h @@ -39,60 +39,73 @@ typedef struct s_linkcell { double x,y,z; /* the actual cell lengthes */ t_list *subcell; /* pointer to the cell lists */ int dnlc; /* direct neighbour lists counter */ + int countn; /* amount of neighbours */ } t_linkcell; #include "visual/visual.h" -# moldyn properties structure */ +# moldyn structure */ typedef struct s_moldyn { int count; /* total amount of atoms */ t_atom *atom; /* pointer to the atoms */ + t_3dvec dim; /* dimensions of the simulation volume */ - /* potential, force & parameters */ - /* potential force funtion created by the user */ - int (*potential_force_function)(struct s_moldyn *moldyn); + /* potential force function pointer and parameters */ + int (*pf_func1b)(struct s_moldyn *,t_atom *); + int (*pf_func2b)(struct s_moldyn *,t_atom *,t_atom *); + int (*pf_func3b)(struct s_moldyn *,t_atom *,t_atom *,t_atom *); + //int (*potential_force_function)(struct s_moldyn *moldyn); void *pot_params; /* parameters describing the potential */ - double cutoff; - double cutoff_square; - /* linked list / cell method */ - t_linkcell lc; - /* temperature */ - double t; - /* integration of newtons equations */ + double cutoff; /* cutoff radius */ + double cutoff_square; /* square of the cutoff radius */ + + t_linkcell lc; /* linked cell method */ + + double t; /* temperature */ + + /* integration function pointer */ int (*integrate)(struct s_moldyn *moldyn); - int time_steps; - double tau; - double tau_square; - /* energy */ - double energy; - /* logging & visualization */ - t_visual vis; - unsigned char lvstat; - unsigned int ewrite; - char efb[64]; - int efd; - unsigned int mwrite; - char mfb[64]; - int mfd; - unsigned int swrite; - char sfb[64]; - int sfd; - unsigned int dwrite; - char dfb[64]; - int dfd; - unsigned int vwrite; - char vfb[64]; - void *visual; - /* moldyn general status */ - unsigned char status; - /* random */ - t_random random; + int time_steps; /* amount of iterations */ + double tau; /* delta t */ + double tau_square; /* delta t squared */ + + double energy; /* energy */ + + t_visual vis; /* visualization/log/save interface structure */ + unsigned char lvstat; /* log & vis properties */ + unsigned int ewrite; /* how often to log energy */ + char efb[64]; /* energy log filename */ + int efd; /* fd for energy log */ + unsigned int mwrite; /* how often to log momentum */ + char mfb[64]; /* momentum log filename */ + int mfd; /* fd for momentum log */ + unsigned int vwrite; /* how often to visualize atom information */ + char vfb[64]; /* visualization file name base */ + void *visual; /* pointer (hack!) */ + unsigned int swrite; /* how often to create a save file */ + + unsigned char status; /* general moldyn properties */ + + t_random random; /* random interface */ } t_moldyn; +#define MOLDYN_LVSTAT_TOTAL_E 0x01 +#define MOLDYN_LVSTAT_TOTAL_M 0x02 +#define MOLDYN_LVSTAT_SAVE 0x04 +#define MOLDYN_LVSTAT_VISUAL 0x08 +#define MOLDYN_LVSTAT_INITIALIZED 0x10 + +#define MOLDYN_STAT_1BP 0x01 +#define MOLDYN_STAT_2BP 0x02 /* define for pair potentials */ +#define MOLDYN_STAT_3BP 0x04 /* define for 3 body pot */ +#define MOLDYN_STAT_PBX 0x08 /* periodic boudaries in x */ +#define MOLDYN_STAT_PBY 0x10 /* y */ +#define MOLDYN_STAT_PBZ 0x20 /* and z direction */ + typedef struct s_ho_params { double spring_constant; double equilibrium_distance; @@ -119,27 +132,17 @@ typedef struct s_tersoff_params { /* general defines */ -#define MOLDYN_LVSTAT_TOTAL_E 0x01 -#define MOLDYN_LVSTAT_TOTAL_M 0x02 -#define MOLDYN_LVSTAT_SAVE 0x04 -#define MOLDYN_LVSTAT_DUMP 0x08 -#define MOLDYN_LVSTAT_VISUAL 0x10 -#define MOLDYN_LVSTAT_INITIALIZED 0x80 - -#define MOLDYN_STAT_POTENTIAL 0x01 -#define MOLDYN_STAT_FORCE 0x02 - #define MOLDYN_TEMP 273.0 #define MOLDYN_TAU 1.0e-15 #define MOLDYN_CUTOFF 10.0e-9 #define MOLDYN_RUNS 1000000 #define MOLDYN_INTEGRATE_VERLET 0x00 -#define MOLDYN_INTEGRATE_DEFAULT MOLDYN_INTEGRATE_VERLET +#define MOLDYN_INTEGRATE_DEFAULT MOLDYN_INTEGRATE_VERLET #define MOLDYN_POTENTIAL_HO 0x00 #define MOLDYN_POTENTIAL_LJ 0x01 -#define MOLDYN_POTENTIAL_DEFAULT MOLDYN_POTENTIAL_LJ +#define MOLDYN_POTENTIAL_DEFAULT MOLDYN_POTENTIAL_LJ /* phsical values */ -- 2.20.1