+ memset(moldyn,0,sizeof(t_moldyn));
+
+ moldyn->argc=argc;
+ moldyn->args=argv;
+
+ rand_init(&(moldyn->random),NULL,1);
+ moldyn->random.status|=RAND_STAT_VERBOSE;
+
+ return 0;
+}
+
+int moldyn_shutdown(t_moldyn *moldyn) {
+
+ printf("[moldyn] shutdown\n");
+
+ moldyn_log_shutdown(moldyn);
+ link_cell_shutdown(moldyn);
+ rand_close(&(moldyn->random));
+ free(moldyn->atom);
+
+ return 0;
+}
+
+int set_int_alg(t_moldyn *moldyn,u8 algo) {
+
+ printf("[moldyn] integration algorithm: ");
+
+ switch(algo) {
+ case MOLDYN_INTEGRATE_VERLET:
+ moldyn->integrate=velocity_verlet;
+ printf("velocity verlet\n");
+ break;
+ default:
+ printf("unknown integration algorithm: %02x\n",algo);
+ printf("unknown\n");
+ return -1;
+ }
+
+ return 0;
+}
+
+int set_cutoff(t_moldyn *moldyn,double cutoff) {
+
+ moldyn->cutoff=cutoff;
+
+ printf("[moldyn] cutoff [A]: %f\n",moldyn->cutoff);
+
+ return 0;
+}
+
+int set_temperature(t_moldyn *moldyn,double t_ref) {
+
+ moldyn->t_ref=t_ref;
+
+ printf("[moldyn] temperature [K]: %f\n",moldyn->t_ref);
+
+ return 0;
+}
+
+int set_pressure(t_moldyn *moldyn,double p_ref) {
+
+ moldyn->p_ref=p_ref;
+
+ printf("[moldyn] pressure [bar]: %f\n",moldyn->p_ref/BAR);
+
+ return 0;
+}
+
+int set_pt_scale(t_moldyn *moldyn,u8 ptype,double ptc,u8 ttype,double ttc) {
+
+ moldyn->pt_scale=(ptype|ttype);
+ moldyn->t_tc=ttc;
+ moldyn->p_tc=ptc;
+
+ printf("[moldyn] p/t scaling:\n");
+
+ printf(" p: %s",ptype?"yes":"no ");
+ if(ptype)
+ printf(" | type: %02x | factor: %f",ptype,ptc);
+ printf("\n");
+
+ printf(" t: %s",ttype?"yes":"no ");
+ if(ttype)
+ printf(" | type: %02x | factor: %f",ttype,ttc);
+ printf("\n");
+
+ return 0;
+}
+
+int set_dim(t_moldyn *moldyn,double x,double y,double z,u8 visualize) {
+
+ moldyn->dim.x=x;
+ moldyn->dim.y=y;
+ moldyn->dim.z=z;
+
+ moldyn->volume=x*y*z;
+
+ if(visualize) {
+ moldyn->vis.dim.x=x;
+ moldyn->vis.dim.y=y;
+ moldyn->vis.dim.z=z;
+ }
+
+ moldyn->dv=0.000001*moldyn->volume;
+
+ printf("[moldyn] dimensions in A and A^3 respectively:\n");
+ printf(" x: %f\n",moldyn->dim.x);
+ printf(" y: %f\n",moldyn->dim.y);
+ printf(" z: %f\n",moldyn->dim.z);
+ printf(" volume: %f\n",moldyn->volume);
+ printf(" visualize simulation box: %s\n",visualize?"yes":"no");
+ printf(" delta volume (pressure calc): %f\n",moldyn->dv);
+
+ return 0;
+}
+
+int set_nn_dist(t_moldyn *moldyn,double dist) {
+
+ moldyn->nnd=dist;
+
+ return 0;
+}
+
+int set_pbc(t_moldyn *moldyn,u8 x,u8 y,u8 z) {
+
+ printf("[moldyn] periodic boundary conditions:\n");
+
+ if(x)
+ moldyn->status|=MOLDYN_STAT_PBX;
+
+ if(y)
+ moldyn->status|=MOLDYN_STAT_PBY;
+
+ if(z)
+ moldyn->status|=MOLDYN_STAT_PBZ;
+
+ printf(" x: %s\n",x?"yes":"no");
+ printf(" y: %s\n",y?"yes":"no");
+ printf(" z: %s\n",z?"yes":"no");
+
+ return 0;
+}
+
+int set_potential1b(t_moldyn *moldyn,pf_func1b func) {
+
+ moldyn->func1b=func;
+
+ return 0;
+}
+
+int set_potential2b(t_moldyn *moldyn,pf_func2b func) {
+
+ moldyn->func2b=func;
+
+ return 0;
+}
+
+int set_potential3b_j1(t_moldyn *moldyn,pf_func2b func) {
+
+ moldyn->func3b_j1=func;
+
+ return 0;
+}
+
+int set_potential3b_j2(t_moldyn *moldyn,pf_func2b func) {
+
+ moldyn->func3b_j2=func;
+
+ return 0;
+}
+
+int set_potential3b_j3(t_moldyn *moldyn,pf_func2b func) {
+
+ moldyn->func3b_j3=func;
+
+ return 0;
+}
+
+int set_potential3b_k1(t_moldyn *moldyn,pf_func3b func) {
+
+ moldyn->func3b_k1=func;
+
+ return 0;
+}
+
+int set_potential3b_k2(t_moldyn *moldyn,pf_func3b func) {
+
+ moldyn->func3b_k2=func;
+
+ return 0;
+}
+
+int set_potential_params(t_moldyn *moldyn,void *params) {
+
+ moldyn->pot_params=params;
+
+ return 0;
+}
+
+int set_avg_skip(t_moldyn *moldyn,int skip) {
+
+ printf("[moldyn] skip %d steps before starting average calc\n",skip);
+ moldyn->avg_skip=skip;
+
+ return 0;
+}
+
+int moldyn_set_log_dir(t_moldyn *moldyn,char *dir) {
+
+ strncpy(moldyn->vlsdir,dir,127);
+
+ return 0;
+}
+
+int moldyn_set_report(t_moldyn *moldyn,char *author,char *title) {
+
+ strncpy(moldyn->rauthor,author,63);
+ strncpy(moldyn->rtitle,title,63);
+
+ return 0;
+}
+
+int moldyn_set_log(t_moldyn *moldyn,u8 type,int timer) {
+
+ char filename[128];
+ int ret;
+
+ printf("[moldyn] set log: ");
+
+ switch(type) {
+ case LOG_TOTAL_ENERGY:
+ moldyn->ewrite=timer;
+ snprintf(filename,127,"%s/energy",moldyn->vlsdir);
+ moldyn->efd=open(filename,
+ O_WRONLY|O_CREAT|O_EXCL,
+ S_IRUSR|S_IWUSR);
+ if(moldyn->efd<0) {
+ perror("[moldyn] energy log fd open");
+ return moldyn->efd;
+ }
+ dprintf(moldyn->efd,"# total energy log file\n");
+ printf("total energy (%d)\n",timer);
+ break;
+ case LOG_TOTAL_MOMENTUM:
+ moldyn->mwrite=timer;
+ snprintf(filename,127,"%s/momentum",moldyn->vlsdir);
+ moldyn->mfd=open(filename,
+ O_WRONLY|O_CREAT|O_EXCL,
+ S_IRUSR|S_IWUSR);
+ if(moldyn->mfd<0) {
+ perror("[moldyn] momentum log fd open");
+ return moldyn->mfd;
+ }
+ dprintf(moldyn->efd,"# total momentum log file\n");
+ printf("total momentum (%d)\n",timer);
+ break;
+ case LOG_PRESSURE:
+ moldyn->pwrite=timer;
+ snprintf(filename,127,"%s/pressure",moldyn->vlsdir);
+ moldyn->pfd=open(filename,
+ O_WRONLY|O_CREAT|O_EXCL,
+ S_IRUSR|S_IWUSR);
+ if(moldyn->pfd<0) {
+ perror("[moldyn] pressure log file\n");
+ return moldyn->pfd;
+ }
+ dprintf(moldyn->pfd,"# pressure log file\n");
+ printf("pressure (%d)\n",timer);
+ break;
+ case LOG_TEMPERATURE:
+ moldyn->twrite=timer;
+ snprintf(filename,127,"%s/temperature",moldyn->vlsdir);
+ moldyn->tfd=open(filename,
+ O_WRONLY|O_CREAT|O_EXCL,
+ S_IRUSR|S_IWUSR);
+ if(moldyn->tfd<0) {
+ perror("[moldyn] temperature log file\n");
+ return moldyn->tfd;
+ }
+ dprintf(moldyn->tfd,"# temperature log file\n");
+ printf("temperature (%d)\n",timer);
+ break;
+ case SAVE_STEP:
+ moldyn->swrite=timer;
+ printf("save file (%d)\n",timer);
+ break;
+ case VISUAL_STEP:
+ moldyn->vwrite=timer;
+ ret=visual_init(&(moldyn->vis),moldyn->vlsdir);
+ if(ret<0) {
+ printf("[moldyn] visual init failure\n");
+ return ret;
+ }
+ printf("visual file (%d)\n",timer);
+ break;
+ case CREATE_REPORT:
+ snprintf(filename,127,"%s/report.tex",moldyn->vlsdir);
+ moldyn->rfd=open(filename,
+ O_WRONLY|O_CREAT|O_EXCL,
+ S_IRUSR|S_IWUSR);
+ if(moldyn->rfd<0) {
+ perror("[moldyn] report fd open");
+ return moldyn->rfd;
+ }
+ printf("report -> ");
+ if(moldyn->efd) {
+ snprintf(filename,127,"%s/e_plot.scr",
+ moldyn->vlsdir);
+ moldyn->epfd=open(filename,
+ O_WRONLY|O_CREAT|O_EXCL,
+ S_IRUSR|S_IWUSR);
+ if(moldyn->epfd<0) {
+ perror("[moldyn] energy plot fd open");
+ return moldyn->epfd;
+ }
+ dprintf(moldyn->epfd,e_plot_script);
+ close(moldyn->epfd);
+ printf("energy ");
+ }
+ if(moldyn->pfd) {
+ snprintf(filename,127,"%s/pressure_plot.scr",
+ moldyn->vlsdir);
+ moldyn->ppfd=open(filename,
+ O_WRONLY|O_CREAT|O_EXCL,
+ S_IRUSR|S_IWUSR);
+ if(moldyn->ppfd<0) {
+ perror("[moldyn] p plot fd open");
+ return moldyn->ppfd;
+ }
+ dprintf(moldyn->ppfd,pressure_plot_script);
+ close(moldyn->ppfd);
+ printf("pressure ");
+ }
+ if(moldyn->tfd) {
+ snprintf(filename,127,"%s/temperature_plot.scr",
+ moldyn->vlsdir);
+ moldyn->tpfd=open(filename,
+ O_WRONLY|O_CREAT|O_EXCL,
+ S_IRUSR|S_IWUSR);
+ if(moldyn->tpfd<0) {
+ perror("[moldyn] t plot fd open");
+ return moldyn->tpfd;
+ }
+ dprintf(moldyn->tpfd,temperature_plot_script);
+ close(moldyn->tpfd);
+ printf("temperature ");
+ }
+ dprintf(moldyn->rfd,report_start,
+ moldyn->rauthor,moldyn->rtitle);
+ printf("\n");
+ break;
+ default:
+ printf("unknown log type: %02x\n",type);
+ return -1;
+ }
+
+ return 0;
+}
+
+int moldyn_log_shutdown(t_moldyn *moldyn) {
+
+ char sc[256];
+
+ printf("[moldyn] log shutdown\n");
+ if(moldyn->efd) {
+ close(moldyn->efd);
+ if(moldyn->rfd) {
+ dprintf(moldyn->rfd,report_energy);
+ snprintf(sc,255,"cd %s && gnuplot e_plot.scr",
+ moldyn->vlsdir);
+ system(sc);
+ }
+ }
+ if(moldyn->mfd) close(moldyn->mfd);
+ if(moldyn->pfd) {
+ close(moldyn->pfd);
+ if(moldyn->rfd)
+ dprintf(moldyn->rfd,report_pressure);
+ snprintf(sc,255,"cd %s && gnuplot pressure_plot.scr",
+ moldyn->vlsdir);
+ system(sc);
+ }
+ if(moldyn->tfd) {
+ close(moldyn->tfd);
+ if(moldyn->rfd)
+ dprintf(moldyn->rfd,report_temperature);
+ snprintf(sc,255,"cd %s && gnuplot temperature_plot.scr",
+ moldyn->vlsdir);
+ system(sc);
+ }
+ if(moldyn->rfd) {
+ dprintf(moldyn->rfd,report_end);
+ close(moldyn->rfd);
+ snprintf(sc,255,"cd %s && pdflatex report >/dev/null 2>&1",
+ moldyn->vlsdir);
+ system(sc);
+ snprintf(sc,255,"cd %s && pdflatex report >/dev/null 2>&1",
+ moldyn->vlsdir);
+ system(sc);
+ snprintf(sc,255,"cd %s && dvipdf report >/dev/null 2>&1",
+ moldyn->vlsdir);
+ system(sc);
+ }
+ if(&(moldyn->vis)) visual_tini(&(moldyn->vis));
+
+ return 0;
+}
+
+/*
+ * creating lattice functions
+ */
+
+int create_lattice(t_moldyn *moldyn,u8 type,double lc,int element,double mass,
+ u8 attr,u8 brand,int a,int b,int c,t_3dvec *origin) {
+
+ int new,count;