git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@341 f3b2605a-c512-4ea7-a41b-209d697bcdaa

tools/Makefile

@@ -25,8 +25,12 @@ micelle2d:	micelle2d.o
 data2xmovie:	data2xmovie.o
 	g++ -g data2xmovie.o -o data2xmovie
 
+thermo_extract:	thermo_extract.o
+	gcc -g thermo_extract.o -o thermo_extract
+
 clean:
 	rm binary2txt replicate restart2data chain micelle2d data2xmovie
+	rm thermo_extract
 	rm *.o
 
 #

tools/thermo_extract.c

@@ -0,0 +1,238 @@
+/* Written by Vikas Varshney
+  Dated Feb 22, 2007
+  Contact Info: vikas.varshney@gmail.com
+
+The main purpose of this simple code is to extract thermodynamic
+information such as Temperature, Pressure, Energy, etc from LAMMPS log
+files, to plot them as a function of timestep in a simple plotting
+programs such as xmgrace.
+
+Such plots are useful at initial stages of a simulation to make sure
+the system is equilibrated.
+
+To run this program please compile it as
+ gcc -O3 thermo_extract.c -lm -o thermo_extract
+
+To extract temperature as a function of timestep, run the code as
+
+thermo_extract -p Temp -s/-m logfile1 logfile2 ... (all the log files)
+
+Time and temperature is output as 2 columns of data.  It can
+be re-directed to a file for plotting.
+
+ -p for thermo parameter to extract
+ -s if the output format is single line, or
+ -m is the output format is multi line
+
+Few points
+
+1. The log file must contain a "thermo N" command where N is the
+  frequency of the thermo output.
+
+2. The name of the property "Temp" (in previous example) has to match
+  the thermo property in the logfile.
+
+3. The log file(s) can contain thermo info for multiple runs.
+
+4. Currently, you can only use one parameter as input, so for extracting
+  multiple properties, you have to run the code again.
+
+5. The Program uses the following keywords to keep track of the data in
+  the file. In general, these keywords are not used in input script (which
+  in turn get printed in log file)  but are worth mentioning. 
+
+  PLEASE avoid using  
+  "Dangerous", "Memory", "Step" and "Loop" in the input script
+
+  "thermo" and "run" except when they are used to specify frequency of 
+   thermo output and total number of steps to be run, respectively.
+
+*/
+
+#include<stdio.h>
+#include<stdlib.h>
+#include<math.h>
+#include <string.h>
+#include <stddef.h>
+
+FILE *input;
+char filename_input[100];
+char string1[100],*string2;
+char temp[80];
+int j,k,check,timestep;
+double datapoint;
+int thermostylecounter,thermocounter,runcounter,totalsteps;
+int narg1;
+char *token;
+char templl[80];
+int thermo[100];
+int run[100];
+
+void scan_first_part()
+{
+ while(strcmp(temp,"Memory"))
+  fscanf(input,"%s ",&temp);
+}
+
+void scan_data_multi(int temp1,char* chartemp)
+{
+ totalsteps=run[temp1]/thermo[temp1]+1;
+ for(j=0;j<totalsteps;j++)
+  {
+    while(strcmp(temp,"Step"))
+      fscanf(input,"%s ",&temp);
+
+    fscanf(input,"%s ",&temp);
+    timestep=atoi(temp);
+
+    while(strcmp(temp,chartemp))
+      fscanf(input,"%s ",&temp);
+
+    fscanf(input,"%s ",&temp);
+    fscanf(input,"%s ",&temp);
+    datapoint=atof(temp);
+    if ((temp1!=0) && (j==0))
+      {}
+    else
+      printf("%d %f\n",timestep,datapoint);
+  }
+}
+
+void scan_data_single(int temp1,char* chartemp)
+{
+ fgets(string1,100,input);
+ fgets(string1,100,input);
+ narg1=0;
+ for(j=0;j<strlen(string1);j++)
+  if(string1[j]==' ')
+    narg1++;
+
+ token=strtok(string1," ");
+ check=0;
+ for(j=1;j<narg1;j++)
+  {
+    token=strtok(NULL," ");
+    if (!strcmp(token,chartemp))
+      {
+        check=j;
+        break;
+      }
+  }
+
+ if (check>0)
+  {}
+ else
+  {
+    printf("Couldn't recognize parameter\n");
+    exit(1);
+  }
+
+ totalsteps=run[temp1]/thermo[temp1]+1;
+ for(j=0;j<totalsteps;j++)
+  {
+    fscanf(input,"%s ",&temp);
+    timestep=atoi(temp);
+    for(k=0;k<check;k++)
+      fscanf(input,"%s ",&temp);
+    datapoint=atof(temp);
+    for(k=0;k<narg1-1-check;k++)
+      fscanf(input,"%s ",&temp);
+    if ((temp1!=0) && (j==0))
+      {}
+    else
+      printf("%d %f\n",timestep,datapoint);
+  }
+}
+
+int main(int arg, char **argv)
+{
+ int singleoutput,next,eofpointer,i,file;
+ char firsttemp[256];
+ int iterations;
+ if (arg<5)
+  {
+    printf("Insufficient number of arguements\n");
+    printf("Please make sure the systax has the following format\n");
+    printf("thermo_extract -p parameter -m/-s logfile1 logfile2 ...\n");
+    exit(1);
+  }
+ for(file=4;file<arg;file++)
+  {
+    sprintf(filename_input,argv[file]);
+    if ((input=fopen(filename_input,"r"))==NULL)
+      {
+        printf("Error reading %dth file.\n",file);
+        exit(1);
+      }
+    iterations=0;
+    while(!feof(input))
+      {
+        fscanf(input,"%s ",&firsttemp);
+        if (!strcmp(firsttemp,"Dangerous"))
+          iterations++;
+      }
+    rewind(input);
+    for(i=0;i<100;i++)
+      {
+        thermo[i]=0;
+        run[i]=0;
+      }
+
+    for(i=0;i<iterations;i++)
+      {
+        while(strcmp(firsttemp,"run"))
+          {
+            fscanf(input,"%s ",&firsttemp);
+            if (!strcmp(firsttemp,"thermo"))
+              {
+                fscanf(input,"%s ",&firsttemp);
+                thermo[i]=atoi(firsttemp);
+              }
+          }
+        fscanf(input,"%s ",&firsttemp);
+        run[i]=atoi(firsttemp);
+        if ((i==0) && (thermo[i]==0))
+          {
+            printf("thermo info not found in the file.. Exiting\n");
+            exit(1);
+          }
+        if (thermo[i]==0)
+          thermo[i]=thermo[i-1];
+      }
+
+    rewind(input);
+
+    if (!strcmp(argv[3],"-m"))
+      thermostylecounter=1;
+    else if (!strcmp(argv[3],"-s"))
+      thermostylecounter=0;
+    else
+      {
+        printf("Couldn't recognize file format. Please use either -m or -s\n");
+        exit(1);
+      }
+
+    if (thermostylecounter==1)
+      for(i=0;i<iterations;i++)
+        {
+	  scan_first_part();
+          scan_data_multi(i,argv[2]);
+          while(strcmp(temp,"Loop"))
+            fscanf(input,"%s ",&temp);
+          for(j=0;j<19;j++)
+            fgets(temp,80,input);
+        }
+    else
+      for(i=0;i<iterations;i++)
+        {
+	  scan_first_part();
+          scan_data_single(i,argv[2]);
+          while(strcmp(temp,"Loop"))
+            fscanf(input,"%s ",&temp);
+          for(j=0;j<19;j++)
+            fgets(temp,80,input);
+        }
+    fclose(input);
+  }
+ return 0;
+}