more testing

diff --git a/clean b/clean
index 34c2b3c..fc5f86d 100755 (executable)
--- a/clean
+++ b/clean
@@ -1 +1 @@
-rm -f saves/* video/*
+rm -f saves/* video/*.ppm video/*.png

diff --git a/doit b/doit
deleted file mode 100755 (executable)
index b9bfa91..0000000
--- a/doit
+++ /dev/null
@@ -1,9 +0,0 @@
-#!/bin/bash
-
-./clean
-gcc -o posic posic.c -Wall
-./posic
-./perms
-rasmol -nodisplay
-./ppm2avi
-mplayer video/md.avi

diff --git a/moldyn.c b/moldyn.c
index f2ac637..0fd1aca 100644 (file)
--- a/moldyn.c
+++ b/moldyn.c
@@ -30,6 +30,7 @@ int moldyn_usage(char **argv) {
        printf("-M <steps> <file> (log total momentum)\n");
        printf("-D <steps> <file> (dump total information)\n");
        printf("-S <steps> <filebase> (single save file)\n");
+       printf("-V <steps> <filebase> (rasmol file)\n");
        printf("--- physics options ---\n");
        printf("-T <temperature> [K] (%f)\n",MOLDYN_TEMP);
        printf("-t <timestep tau> [s] (%f)\n",MOLDYN_TAU);
@@ -70,9 +71,13 @@ int moldyn_parse_argv(t_moldyn *moldyn,int argc,char **argv) {
                                        moldyn->swrite=atoi(argv[++i]);
                                        strncpy(moldyn->sfb,argv[++i],64);
                                        break;
-                               case 'T':
+                               case 'V':
+                                       moldyn->vwrite=atoi(argv[++i]);
+                                       strncpy(moldyn->vfb,argv[++i],64);
                                        break;
+                               case 'T':
                                        moldyn->t=atof(argv[++i]);
+                                       break;
                                case 't':
                                        moldyn->tau=atof(argv[++i]);
                                        break;
@@ -93,9 +98,12 @@ int moldyn_parse_argv(t_moldyn *moldyn,int argc,char **argv) {
        return 0;
 }
 
-int moldyn_log_init(t_moldyn *moldyn) {
+int moldyn_log_init(t_moldyn *moldyn,void *v) {
 
        moldyn->lvstat=0;
+       t_visual *vis;
+
+       vis=v;
 
        if(moldyn->ewrite) {
                moldyn->efd=open(moldyn->efb,O_WRONLY|O_CREAT|O_TRUNC);
@@ -130,8 +138,23 @@ int moldyn_log_init(t_moldyn *moldyn) {
                moldyn->lvstat|=MOLDYN_LVSTAT_DUMP;
        }
 
-       if(moldyn->dwrite)
+       if((moldyn->vwrite)&&(vis)) {
+               moldyn->visual=vis;
+               visual_init(vis,moldyn->vfb);
                moldyn->lvstat|=MOLDYN_LVSTAT_VISUAL;
+       }
+
+       moldyn->lvstat|=MOLDYN_LVSTAT_INITIALIZED;
+
+       return 0;
+}
+
+int moldyn_shutdown(t_moldyn *moldyn) {
+
+       if(moldyn->efd) close(moldyn->efd);
+       if(moldyn->mfd) close(moldyn->efd);
+       if(moldyn->dfd) close(moldyn->efd);
+       if(moldyn->visual) visual_tini(moldyn->visual);
 
        return 0;
 }
@@ -328,7 +351,6 @@ int moldyn_integrate(t_moldyn *moldyn) {
 
        int i;
        unsigned int e,m,s,d,v;
-       unsigned char lvstat;
        t_3dvec p;
 
        int fd;
@@ -340,7 +362,7 @@ int moldyn_integrate(t_moldyn *moldyn) {
        d=moldyn->dwrite;
        v=moldyn->vwrite;
 
-       if(!(lvstat&MOLDYN_LVSTAT_INITIALIZED)) {
+       if(!(moldyn->lvstat&MOLDYN_LVSTAT_INITIALIZED)) {
                printf("[moldyn] warning, lv system not initialized\n");
                return -1;
        }

diff --git a/moldyn.h b/moldyn.h
index cbfc173..42764c5 100644 (file)
--- a/moldyn.h
+++ b/moldyn.h
@@ -10,7 +10,6 @@
 
 #include "math/math.h"
 #include "random/random.h"
-//#include "visual/visual.h"
 
 /* datatypes */
 
@@ -55,6 +54,7 @@ typedef struct s_moldyn {
        char dfb[64];
        int dfd;
        unsigned int vwrite;
+       char vfb[64];
        void *visual;
        /* moldyn general status */
        unsigned char status;
@@ -112,7 +112,8 @@ typedef struct s_lj_params {
 
 int moldyn_usage(char **argv);
 int moldyn_parse_argv(t_moldyn *moldyn,int argc,char **argv);
-int moldyn_log_init(t_moldyn *moldyn);
+int moldyn_log_init(t_moldyn *moldyn,void *v);
+int moldyn_shutdown(t_moldyn *moldyn);
 
 int create_lattice(unsigned char type,int element,double mass,double lc,
                    int a,int b,int c,t_atom **atom);

diff --git a/posic.c b/posic.c
index 7c1c418..f026abe 100644 (file)
--- a/posic.c
+++ b/posic.c
@@ -17,25 +17,25 @@
 int main(int argc,char **argv) {
 
        t_moldyn md;
-
        t_atom *si;
-
        t_visual vis;
-
        t_random random;
 
        int a,b,c;
-       double t,e,u;
+       double e,u;
        double help;
        t_3dvec p;
        int count;
 
        t_lj_params lj;
+       t_ho_params ho;
 
-       char fb[32]="saves/lj_test";
+       /* parse arguments */
+       a=moldyn_parse_argv(&md,argc,argv);
+       if(a<0) return -1;
 
        /* init */
-
+       moldyn_log_init(&md,&vis);
        rand_init(&random,NULL,1);
        random.status|=RAND_STAT_VERBOSE;
 
@@ -44,40 +44,54 @@ int main(int argc,char **argv) {
        //      printf("%f %f\n",rand_get_gauss(&random),
        //                       rand_get_gauss(&random));
 
-       visual_init(&vis,fb);
-
        a=LEN_X;
        b=LEN_Y;
        c=LEN_Z;
 
        /* set for 'bounding atoms' */
-       //vis.dim.x=a*LC_SI;
-       //vis.dim.y=b*LC_SI;
-       //vis.dim.z=c*LC_SI;
-
-       t=TEMPERATURE;
+       vis.dim.x=a*LC_SI;
+       vis.dim.y=b*LC_SI;
+       vis.dim.z=c*LC_SI;
 
+       /* init lattice
        printf("placing silicon atoms ... ");
        count=create_lattice(DIAMOND,SI,M_SI,LC_SI,a,b,c,&si);
-       printf("(%d) ok!\n",count);
-
-       /* testing purpose
+       printf("(%d) ok!\n",count); */
+       /* testing purpose */
        count=2;
        si=malloc(2*sizeof(t_atom));
-       si[0].r.x=0.16e-9;
+       si[0].r.x=0.35*sqrt(3.0)*LC_SI/2.0;
        si[0].r.y=0;
        si[0].r.z=0;
        si[0].element=SI;
        si[0].mass=M_SI;
-       si[1].r.x=-0.16e-9;
+       si[1].r.x=-si[0].r.x;
        si[1].r.y=0;
        si[1].r.z=0;
        si[1].element=SI;
        si[1].mass=M_SI;
-       */
+       /* */
+
+       /* moldyn init (now si is a valid address) */
+       md.count=count;
+       md.atom=si;
+       md.potential=potential_lennard_jones;
+       md.force=force_lennard_jones;
+       //md.potential=potential_harmonic_oscillator;
+       //md.force=force_harmonic_oscillator;
+       md.cutoff=R_CUTOFF;
+       md.cutoff_square=(R_CUTOFF*R_CUTOFF);
+       md.pot_params=&lj;
+       //md.pot_params=&ho;
+       md.integrate=velocity_verlet;
+       //md.time_steps=RUNS;
+       //md.tau=TAU;
+       md.status=0;
+       md.visual=&vis;
 
-       printf("setting thermal fluctuations\n");
-       thermal_init(si,&random,count,t);
+       printf("setting thermal fluctuations (T=%f K)\n",md.t);
+       //thermal_init(&md,&random,count);
+       for(a=0;a<count;a++) v3_zero(&(si[0].v));
        //v3_zero(&(si[0].v));
        //v3_zero(&(si[1].v));
 
@@ -85,33 +99,22 @@ int main(int argc,char **argv) {
 
        e=get_e_kin(si,count);
        printf("kinetic energy: %.40f [J]\n",e);
-       printf("3/2 N k T = %.40f [J]\n",1.5*count*K_BOLTZMANN*t);
+       printf("3/2 N k T = %.40f [J]\n",1.5*count*K_BOLTZMANN*md.t);
 
        /* check total momentum */
        p=get_total_p(si,count);
        printf("total momentum: %.30f [Ns]\n",v3_norm(&p));
 
        /* check potential energy */
-       md.count=count;
-       md.atom=si;
-       md.potential=potential_lennard_jones;
-       md.force=force_lennard_jones;
-       md.cutoff=R_CUTOFF;
-       md.cutoff_square=(R_CUTOFF*R_CUTOFF);
-       md.pot_params=&lj;
-       md.integrate=velocity_verlet;
-       md.time_steps=RUNS;
-       md.tau=TAU;
-       md.status=0;
-       md.visual=&vis;
-       md.write=WRITE_FILE;
-
        lj.sigma6=LJ_SIGMA_SI*LJ_SIGMA_SI;
        help=lj.sigma6*lj.sigma6;
        lj.sigma6*=help;
        lj.sigma12=lj.sigma6*lj.sigma6;
        lj.epsilon=LJ_EPSILON_SI;
 
+       ho.equilibrium_distance=0.25*sqrt(3.0)*LC_SI;
+       ho.spring_constant=LJ_EPSILON_SI;
+
        u=get_e_pot(&md);
 
        printf("potential energy: %.40f [J]\n",u);
@@ -123,7 +126,7 @@ int main(int argc,char **argv) {
        md.dim.z=c*LC_SI;
 
        printf("estimated accurate time step: %.30f [s]\n",
-              estimate_time_step(&md,3.0,t));
+              estimate_time_step(&md,3.0,md.t));
 
 
        /*
@@ -139,9 +142,9 @@ int main(int argc,char **argv) {
 
        /* close */
 
-       visual_tini(&vis);
-
        rand_close(&random);
+
+       moldyn_shutdown(&md);
        
        return 0;
 }

diff --git a/ppm2avi b/ppm2avi
index febe86c..be4c6dd 100755 (executable)
--- a/ppm2avi
+++ b/ppm2avi
@@ -1,7 +1,5 @@
-#!/bin/bash
-
-for i in video/*.ppm; do
-       convert $i video/$(basename $i ppm)png
+for i in saves/*.ppm; do
+       convert $i saves/$(basename $i ppm)png
 done
 
-mencoder mf://video/*.png -ovc copy -o video/md.avi
+mencoder mf://saves/*.png -ovc copy -o video/md.avi