From e1348f10aff2c0bb1040108181d13fcb48db5af2 Mon Sep 17 00:00:00 2001
From: hackbard <hackbard@sage.physik.uni-augsburg.de>
Date: Mon, 23 Jul 2007 17:09:26 +0200
Subject: [PATCH] added postproc stuff, sic mods (today i was a lazy ass!)

---
 Makefile   |   7 ++-
 moldyn.c   |   5 +-
 moldyn.h   |   3 +
 postproc.c | 166 +++++++++++++++++++++++++++++++++++++++++++++++++++++
 sic.c      |  19 ++++--
 5 files changed, 191 insertions(+), 9 deletions(-)

diff --git a/Makefile b/Makefile
index 72904f5..ee6e927 100644
--- a/Makefile
+++ b/Makefile
@@ -16,11 +16,14 @@ POT_SRC=potentials/tersoff.c
 POT_SRC+=potentials/albe.c
 POT_SRC+= potentials/lennard_jones.c potentials/harmonic_oscillator.c
 
-all: sic fluctuation_calc
+all: sic fluctuation_calc postproc
 
 sic: 
 	$(CC) $(CFLAGS) $(LDFLAGS) $(POT_SRC) $(SOURCE) sic.c -o sic
 
+postproc:
+	$(CC) $(CFLAGS) $(LDFLAGS) $(POT_SRC) $(SOURCE) postproc.c -o postproc
+
 .PHONY:clean
 clean:
-	rm -f sic
+	rm -f sic postproc
diff --git a/moldyn.c b/moldyn.c
index 7d27965..a310e91 100644
--- a/moldyn.c
+++ b/moldyn.c
@@ -24,6 +24,9 @@ int moldyn_init(t_moldyn *moldyn,int argc,char **argv) {
 
 	memset(moldyn,0,sizeof(t_moldyn));
 
+	moldyn->argc=argc;
+	moldyn->args=argv;
+
 	rand_init(&(moldyn->random),NULL,1);
 	moldyn->random.status|=RAND_STAT_VERBOSE;
 
@@ -1483,7 +1486,7 @@ return 0;
 	printf("\rsched:%d, steps:%d, T:%3.1f/%3.1f P:%4.1f/%4.1f V:%6.1f",
 	       sched->count,i,
 	       moldyn->t,moldyn->t_avg,
-	       moldyn->p_avg/BAR,moldyn->p/BAR,
+	       moldyn->p_avg/BAR,moldyn->gp_avg/BAR,
 	       moldyn->volume);
 	fflush(stdout);
 		}
diff --git a/moldyn.h b/moldyn.h
index a595585..9f9d0f7 100644
--- a/moldyn.h
+++ b/moldyn.h
@@ -78,6 +78,9 @@ typedef struct s_moldyn_schedule {
 
 /* moldyn main structure */
 typedef struct s_moldyn {
+	int argc;		/* number of arguments */
+	char **args;		/* pointer to arguments */
+
 	int count;		/* total amount of atoms */
 	double mass;		/* total system mass */
 	t_atom *atom;		/* pointer to the atoms */
diff --git a/postproc.c b/postproc.c
index 68e0918..18834af 100644
--- a/postproc.c
+++ b/postproc.c
@@ -5,15 +5,181 @@
  *
  */
 
+#define _GNU_SOURCE
+#include <stdio.h>
+#include <unistd.h>
+#include <stdlib.h>
+#include <sys/types.h>
+#include <sys/stat.h>
+#include <fcntl.h>
+
 #include <math.h>
  
 #include "moldyn.h"
+#include "math/math.h"
+
+#define FILEMAX	127
+#define BUFMAX	127
+
+#define DISPLACEMENT	(1<<0)
+#define VELOCITY	(1<<1)
+
+static char *pse[]={
+        "*",
+        "H",
+        "He",
+        "Li",
+        "Be",
+        "B",
+        "C",
+        "N",
+        "O",
+        "F",
+        "Ne",
+        "Na",
+        "Mg",
+        "Al",
+        "Si",
+        "P",
+        "S",
+        "Cl",
+        "Ar",
+};
+
+int usage(void) {
+	printf("usage:\n");
+	printf("  -i <infile> -o <outfile>\n");
+	printf("  -d/v (displacement,velocity)\n");
+	printf(" \n");
+	return 1;
+}
 
 int main(int argc,char **argv) {
 
 	t_moldyn md;
+	t_atom *atom;
+	char infile[FILEMAX+1];
+	int infd;
+	char outfile[FILEMAX+1];
+	int outfd;
+	int ret,size;
+	unsigned char mode;
+	char buf[BUFMAX+1];
+	t_3dvec dist;
+	int i;
+
+	memset(infile,0,FILEMAX+1);
+	memset(outfile,0,FILEMAX+1);
+	memset(buf,0,BUFMAX+1);
+	mode=0;
+
+	/* parse argv */
+	for(i=1;i<argc;i++) {
+
+		if(argv[i][0]!='-') {
+			usage();
+			return -1;
+		}
+		
+		switch(argv[i][1]) {
+			case 'h':
+				usage();
+				return 1;
+			case 'i':
+				strncpy(infile,argv[++i],FILEMAX);
+				break;
+			case 'o':
+				strncpy(outfile,argv[++i],FILEMAX);
+				break;
+			case 'd':
+				mode=DISPLACEMENT;
+				break;
+			case 'v':
+				mode=VELOCITY;
+				break;
+			default:
+				usage();
+				return -1;
+		}
+
+	}
+
+	/* open infile */
 
+	if(!strcmp(infile,"")) {
+		printf("no infile specified!\n");
+		return -1;
+	}
+	printf("infile -> %s\n",infile);
+
+	infd=open(infile,O_RDONLY);
+	if(infd<3) {
+		perror("infile");
+		return infd;
+	}
+
+	/* open outfile */
 	
+	if(!strcmp(outfile,"")) {
+		printf("no outfile specified!\n");
+		return -1;
+	}
+	printf("outfile -> %s\n",outfile);
+
+	outfd=open(outfile,O_WRONLY|O_CREAT);
+	if(outfd<3) {
+		perror("outfile");
+		return outfd;
+	}
+
+	/* read in data */
+
+	size=sizeof(t_moldyn);
+	ret=0;
+	while(size-ret)
+		ret+=read(infd,&md,size-ret);
+	printf("read %d bytes moldyn struct data\n",size);
+
+	/* allocate memory for atoms */
+	size=md.count*sizeof(t_atom);
+	md.atom=malloc(size);
+	if(md.atom==NULL) {
+		perror("malloc");
+		goto end;
+	}
+
+	/* read in atom data */
+
+	ret=0;
+	atom=md.atom;
+	while(size-ret)
+		ret+=read(infd,atom,size-ret);
+	printf("read %d bytes atom data\n",size);
+
+	/* postprocess ... */
+	dprintf(outfd,"%d\n",md.count+8);
+	dprintf(outfd,"atoms at time %f\n",md.time);
+	for(i=0;i<md.count;i++) {
+printf("%d ",i);
+		dprintf(outfd,"%s %f %f %f",pse[atom[i].element],
+		                           atom[i].r.x,atom[i].r.y,atom[i].r.z);
+		if(mode&DISPLACEMENT) {
+			v3_sub(&dist,&(atom[i].r),&(atom[i].r_0));
+			check_per_bound(&md,&dist);
+			dprintf(outfd," %f",v3_norm(&dist));
+		}
+		if(mode&VELOCITY) {
+			dprintf(outfd," %f",atom[i].ekin);
+		}
+		dprintf(outfd,"\n");
+	}
+
+	/* free memory & close file descriptors */
+
+end:
+	free(md.atom);
+	close(infd);
+	close(outfd);
 
 	return 0;
 }
diff --git a/sic.c b/sic.c
index 5f2a8db..fa2a396 100644
--- a/sic.c
+++ b/sic.c
@@ -23,13 +23,15 @@
 
 #define INJECT		1
 #define NR_ATOMS	1
-#define R_C		2.0
+#define R_C		1.0
 #define T_C		10.0
-#define LCNT		2
+#define LCNT		5
 
 typedef struct s_hp {
 	int a_count;	/* atom count */
 	u8 quit;	/* quit mark */
+	int argc;	/* arg count */
+	char **argv;	/* args */
 } t_hp;
 
 int hook(void *moldyn,void *hook_params) {
@@ -75,6 +77,9 @@ int hook(void *moldyn,void *hook_params) {
 			r.x=(rand_get_double(&(md->random))-0.5)*md->dim.x*0.37;
 			r.y=(rand_get_double(&(md->random))-0.5)*md->dim.y*0.37;
 			r.z=(rand_get_double(&(md->random))-0.5)*md->dim.z*0.37;
+			//r.x=(1.0*atoi(hp->argv[3])-4.5)/9.0*ALBE_LC_SI;
+			//r.y=(1.0*atoi(hp->argv[4])-4.5)/9.0*ALBE_LC_SI;
+			//r.z=(1.0*atoi(hp->argv[5])-4.5)/9.0*ALBE_LC_SI;
 			/* assume valid coordinates */
 			run=0;
 			for(i=0;i<md->count;i++) {
@@ -104,10 +109,10 @@ int hook(void *moldyn,void *hook_params) {
 int main(int argc,char **argv) {
 
 	/* check argv */
-	if(argc!=3) {
-		printf("[sic] usage: %s <logdir> <temperatur>\n",argv[0]);
-		return -1;
-	}
+	//if(argc!=3) {
+	//	printf("[sic] usage: %s <logdir> <temperatur>\n",argv[0]);
+	//	return -1;
+	//}
 
 	/* main moldyn structure */
 	t_moldyn md;
@@ -352,6 +357,8 @@ int main(int argc,char **argv) {
 
 	/* schedule hook function */
 	memset(&hookparam,0,sizeof(t_hp));
+	hookparam.argc=argc;
+	hookparam.argv=argv;
 	moldyn_set_schedule_hook(&md,&hook,&hookparam);
 
 	/* activate logging */
-- 
2.20.1