From 79602bac2da43afa013629dae1d050f499dba7ce Mon Sep 17 00:00:00 2001
From: sjplimp <sjplimp@f3b2605a-c512-4ea7-a41b-209d697bcdaa>
Date: Thu, 22 Feb 2007 19:57:04 +0000
Subject: [PATCH] git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@341
f3b2605a-c512-4ea7-a41b-209d697bcdaa
---
tools/Makefile | 4 +
tools/thermo_extract.c | 238 +++++++++++++++++++++++++++++++++++++++++
2 files changed, 242 insertions(+)
create mode 100644 tools/thermo_extract.c
diff --git a/tools/Makefile b/tools/Makefile
index 599184471b..6e4c93e925 100644
--- a/tools/Makefile
+++ b/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
#
diff --git a/tools/thermo_extract.c b/tools/thermo_extract.c
new file mode 100644
index 0000000000..f79da3aca9
--- /dev/null
+++ b/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;
+}
--
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