forked from lijiext/lammps
Added xmgrace folder
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@10817 f3b2605a-c512-4ea7-a41b-209d697bcdaa
This commit is contained in:
athomps
parent
e7972a6472
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This directory contains a collection of scripts for generating xmgrace plots.
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To use any of these tools, you will probably first need to
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install the xmgrace plotting package:
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http://plasma-gate.weizmann.ac.il/Grace/
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Here is a brief description of the files:
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lammpsplot.cpp: a C++ program that converts log files to xmgrace with labels
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lammpsplot.pdf: documentation for lammpsplot
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logplotawk.oneliner: an awk command that pipes a log file to xmgrace
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logplotgrep.oneliner: a grep command that pipes a log file to xmgrace
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plotthermodata.awk: an awk program that converts log files to xmgrace with labels
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// By Vikas Varshney @ vv0210 at gmail dot com
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#include <stdlib.h>
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#include <iostream>
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#include <fstream.h>
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#include <string>
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#include <vector>
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#include <cctype>
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#include <cstdlib>
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#include <map>
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#include <iomanip>
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#include <algorithm>
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#include <math.h>
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using namespace std;
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using std::cout;
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using std::cin;
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using std::endl;
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using std::string;
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using std::cerr;
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using std::vector;
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typedef vector<string> sentence;
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typedef vector<sentence> filedata;
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typedef string::size_type s_type;
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vector<filedata> f;
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class fd {
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public:
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string filename;
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string property;
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vector <float> value;
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};
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/* This function splits the sentence into array of strings seperated by " "*/
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sentence split(const string& s) {
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sentence a;
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s_type i=0;
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while (i!=s.size()) {
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while (i!=s.size() && isspace(s[i])) {
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++i;
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}
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s_type j=i;
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while (j!=s.size() && !isspace(s[j]))
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++j;
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if (i!=j) {
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a.push_back(s.substr(i,j-i));
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i=j;
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}
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}
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return a;
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}
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/* This function add array of strings (passed as string) to a sentence */
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sentence add_strings(sentence& temp_entry, const string l) {
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sentence temp=split(l);
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s_type mm;
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if (temp.size()!=0)
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for (mm=0;mm!=temp.size();mm++)
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temp_entry.push_back(temp[mm]);
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else
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return temp_entry;
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return temp_entry;
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}
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/* This function reads the logfile produced by lammps */
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void readlogfile_multi(filedata& atemp, ifstream& input, int leave_index) {
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const string ll("----------------");
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const string step("Step");
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const string Mem("Memory");
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const string Loop("Loop");
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int leave=0;
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string line;
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s_type kk=0,mm,kkk;
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s_type length;
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int style;
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int halffile=0;
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while (getline(input,line)) {
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sentence entry=split(line);
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if (entry.size()!=0)
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// Find keyword Memory
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if (!entry[0].compare(Mem)) {
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getline(input,line);
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entry=split(line);
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// Style = 1 means multi line format and style = 2 means single line format
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if (!entry[0].compare(ll)) style=1; else if (!entry[0].compare(step)) style=2; else cout << "style not matching" << endl;
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switch (style) {
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case 1: {
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// Read the line till ll comes up next and store it in a variable.
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sentence zero;
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sentence one;
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zero.push_back(entry[1]);
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one.push_back(entry[2]);
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getline(input,line);
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entry=split(line);
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do {
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if (entry.size()!=0)
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for(int i=0;i<entry.size();i+=3) {
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zero.push_back(entry[i]);
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one.push_back(entry[i+2]);
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}
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getline(input,line);
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entry=split(line);
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if (!entry[0].compare(Loop))
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break;
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}
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while (entry[0].compare(ll));
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if (!atemp.size())
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atemp.push_back(zero);
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atemp.push_back(one);
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int length=zero.size();
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int t=0;
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// Read all the lines till Loop comes up.
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while (entry[0].compare(Loop)) {
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t++;
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sentence a1;
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a1.push_back(entry[2]);
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for(int j=0;j<(length+1)/3;j++) {
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if (!getline(input,line)) {
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halffile=1;
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break;
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}
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entry=split(line);
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for(int i=0;i<entry.size();i+=3)
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a1.push_back(entry[i+2]);
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}
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if (a1.size()==length)
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atemp.push_back(a1);
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if (halffile)
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break;
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if (!getline(input,line))
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break;
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else
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entry=split(line);
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}
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break;
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}
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case 2:
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{
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sentence zero;
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for(int i=0;i!=entry.size();i++)
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zero.push_back(entry[i]);
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getline(input,line);
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entry=split(line);
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if (!atemp.size())
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atemp.push_back(zero);
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int length=zero.size();
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while(entry[0].compare(Loop)) {
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sentence a1;
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for(int i=0;i!=entry.size();i++)
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a1.push_back(entry[i]);
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atemp.push_back(a1);
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getline(input,line);
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entry=split(line);
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if (entry.size()<length) break;
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}
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break;
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}
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}
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if (leave_index>leave) {
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atemp.clear();
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leave++;
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}
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}
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}
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}
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/* This function1 searches for a string in a sentence and return true/false*/
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bool search_string(string str, sentence sen, int& j) {
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j=0;
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while (j!=sen.size()) {
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if (!sen[j].compare(str)) {
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break;
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}
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j++;
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}
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if (j==sen.size()) return false; else return true;
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}
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/* This function is used to ask user to input parameters to be plotted*/
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sentence get_userinput() {
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string temp;
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sentence t;
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cout << "Enter the parameter(s) of which you want the plot for files, read successfully:" << endl;
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getline(cin,temp);
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t=split(temp);
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if (!t[1].compare("cross"))
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if (t.size()!=4) {
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cout << "Currently only two cross parameters can be plotted \nThe syntax is s/p cross param1 param2\n" << endl;
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exit(1);
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}
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return t;
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}
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/*This function replaces certain input keywords to their appropriate words found in lammps file*/
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void transform_userinput(sentence& temp) {
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if (temp.size()) {
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for(int i=1;i!=temp.size();i++) {
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if (!temp[i].compare("t")) temp[i].replace(0,temp[i].length(),"Temp");
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if (!temp[i].compare("p")) temp[i].replace(0,temp[i].length(),"Press");
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if (!temp[i].compare("v")) temp[i].replace(0,temp[i].length(),"Volume");
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if (!temp[i].compare("vd")) temp[i].replace(0,temp[i].length(),"E_vdwl");
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if (!temp[i].compare("te")) temp[i].replace(0,temp[i].length(),"TotEng");
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if (!temp[i].compare("ke")) temp[i].replace(0,temp[i].length(),"KinEng");
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if (!temp[i].compare("pe")) temp[i].replace(0,temp[i].length(),"PotEng");
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if (!temp[i].compare("be")) temp[i].replace(0,temp[i].length(),"E_bond");
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if (!temp[i].compare("ae")) temp[i].replace(0,temp[i].length(),"E_angle");
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if (!temp[i].compare("de")) temp[i].replace(0,temp[i].length(),"E_dihed");
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if (!temp[i].compare("ce")) temp[i].replace(0,temp[i].length(),"E_coul");
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if (!temp[i].compare("le")) temp[i].replace(0,temp[i].length(),"E_long");
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}
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}
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}
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/* This function searches if the parameter is present in the lammps file and return a array of
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associated with the parameter stored in string */
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map<string, vector<int> > update2_userinput(sentence temp) {
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if ((!temp[0].compare("s")) || (!temp[0].compare("p"))) {
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s_type j;
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int jtemp;
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int notfind;
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int notfindall=1;
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map<string, vector<int> > ret;
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sentence::iterator tb=temp.begin();
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for(j=0;j!=f.size();j++)
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ret[*tb].push_back(0);
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tb++;
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for(sentence::iterator aa=tb; aa!=temp.end(); aa++) {
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notfind=1;
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for(j=0;j!=f.size();j++) {
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if (search_string(*aa,f[j][0],jtemp)) {
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ret[*aa].push_back(jtemp);
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notfind=0;
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notfindall=0;
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}
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else
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ret[*aa].push_back(0);
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}
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if (notfind) {
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temp.erase(aa);
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aa--;
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}
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}
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if (notfindall) {
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cerr << "\nDid not find any matching parameters in any input files, read successfully. Please check!!!\n\n";
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exit(1);
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}
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return ret;
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}
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else {
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cerr << "\nFirst string should be s (for series) or p (for parallel)\n\n" << endl;
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exit(1);
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}
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}
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/* This function just print out a line with string str on standard output*/
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void print_line(string str) {
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for(int i=0;i<100;i++)
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cout << str;
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cout << endl;
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}
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/*This function reads the data from the input files*/
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void read_input(int argc, char** argv, sentence& sf,string& analysisfile) {
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filedata a;
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int success_filecounter=0;
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int leave_index=0;
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// Read the data into the file.
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for (int i=1; i<argc; ++i) {
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if (!strcmp(argv[i],"-leave")) {
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leave_index=atoi(argv[i+1]);
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i++;
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continue;
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}
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if (!strcmp(argv[i],"-analysis")) {
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analysisfile=argv[i+1];
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i++;
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continue;
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}
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ifstream in(argv[i]);
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if (in) {
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sf.push_back(argv[i]);
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cout << "Reading file : " << argv[i] << endl;
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if (a.size())
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a.clear();
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readlogfile_multi(a,in,leave_index);
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f.push_back(a);
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in.close();
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success_filecounter++;
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} else {
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cerr << "Cannot open file: " << argv[i] << endl;
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}
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}
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if(!success_filecounter)
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exit(1);
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else {
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sentence aa;
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int exists;
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cout << endl;
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cout << "Select parameters to plot from following: --- " << endl;
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for (int i=0;i<success_filecounter;i++) {
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for(int j=0;j<f[i][0].size();j++) {
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exists=0;
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for(int k=0;k!=aa.size();k++)
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if (!f[i][0][j].compare(aa[k])) {
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exists=1;
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break;
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}
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if (!exists)
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aa.push_back(f[i][0][j]);
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}
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}
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for(int k=0;k!=aa.size();k++) {
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if (!aa[k].compare("Temp")) aa[k].replace(0,aa[k].length(),"Temp(t)");
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if (!aa[k].compare("Press")) aa[k].replace(0,aa[k].length(),"Press(p)");
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if (!aa[k].compare("Volume")) aa[k].replace(0,aa[k].length(),"Volume(v)");
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if (!aa[k].compare("E_vdwl")) aa[k].replace(0,aa[k].length(),"E_vdwl(vd)");
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if (!aa[k].compare("TotEng")) aa[k].replace(0,aa[k].length(),"TotEng(te)");
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if (!aa[k].compare("KinEng")) aa[k].replace(0,aa[k].length(),"KinEng(ke)");
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if (!aa[k].compare("PotEng")) aa[k].replace(0,aa[k].length(),"PotEng(pe)");
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if (!aa[k].compare("E_bond")) aa[k].replace(0,aa[k].length(),"E_bond(be)");
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if (!aa[k].compare("E_angle")) aa[k].replace(0,aa[k].length(),"E_angle(ae)");
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if (!aa[k].compare("E_dihed")) aa[k].replace(0,aa[k].length(),"E_dihed(de)");
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if (!aa[k].compare("E_coul")) aa[k].replace(0,aa[k].length(),"E_coul(ce)");
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if (!aa[k].compare("E_long")) aa[k].replace(0,aa[k].length(),"E_long(le)");
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cout << aa[k];
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if (aa[k].size()<8) cout << "\t";
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cout << "\t";
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if (k%6==5) cout << endl;
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}
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cout << "\n--------------\n\n";
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cout << "Please enter your parameters in the following format: --- " << endl;
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cout << "1. First string should be 'p' or 's' for plotting parameters from different files in parallel or series" << endl;
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cout << "2. Please enter one or more parameters listed above after entering the first string." << endl;
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cout << "3. For certain parameters, short forms may be used as listed in bracket above" << endl;
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cout << " ----- Example: To plot total energy, please type 'p te'." << endl;
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cout << "4. In order to plot one parameter with respect to other, please type 'cross' after p/s followed by two parameters" << endl;
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cout << "5. The independent parameter could be 'Step' as mentioned above." << endl;
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cout << "6. Currently, only two parameters can be plotted with respect to each other." << endl;
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cout << " ----- Example: To plot temperature vs. pressure p cross t p" << endl ;
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cout << "--------------\n\n";
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cout << "For analysis, please exit and use -analysis flag with filename. The file should contain atleast one of these commands: --- " << endl;
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cout << "1. average all/single_filename startvalue(start) endvalue(end)" << endl;
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cout << "2. scale filename property factor" << endl;
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cout << "3. inverse filename property" << endl;
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cout << "4. write Under Coding" << endl;
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cout << "5. subtract property1 property2 filename outputpropertyname" << endl;
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cout << "6. add Under Coding" << endl;
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cout << "--------------\n\n";
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}
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}
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string print_space(int t) {
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string f;
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for (int i=0;i!=t;i++)
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f.push_back(' ');
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return f;
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}
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/*This function prints out the parameter associated index in successfully read file */
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void print_file_index_output(sentence s, map<string, vector<int> > x, sentence sf) {
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size_t maxlen=0;
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for(int i=0;i!=sf.size();i++)
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maxlen=max(maxlen,sf[i].length());
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cout << print_space(maxlen+11);
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for(sentence::iterator aa=++s.begin(); aa!=s.end(); aa++)
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cout << *aa << "\t";
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cout << endl;
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for(int j=0;j!=f.size();j++) {
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cout << "File-> " << sf[j] << print_space(maxlen-sf[j].length()+1) <<": ";
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for(sentence::iterator aa=++s.begin(); aa!=s.end(); aa++) {
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cout << x[*aa][j] << "\t";
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}
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cout << endl;
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}
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}
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void plot_xmgrace(sentence s, vector <fd> data) {
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ofstream out("temp");
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// Some string definitions
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string s1 = "@ s";
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string s2 = " comment ";
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string s3 = " legend ";
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int plotiterator=0; int set; int style;
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int half_data=data.size()/2;
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// Printing out X and Y axis properties
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out << "@ xaxis label char size 1.500000\n";
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out << "@ xaxis ticklabel char size 1.250000\n";
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if (s[1].compare("cross"))
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out << "@ xaxis label " << "\"time\""<< endl;
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else
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out << "@ xaxis label " << "\"" << s[2] << "\""<< endl;
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out << "@ yaxis label char size 1.500000\n";
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out << "@ yaxis ticklabel char size 1.250000\n";
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// Printing out legend properties
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out << "@ legend box linestyle 0\n";
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out << "@ legend 0.25, 0.8\n";
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// Selecting style for series or parallel plotting.
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if (!s[0].compare("s")) style=1; else style=2;
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if (s[1].compare("cross")) {
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if (s.size()==2) {
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out << "@ yaxis label " << "\"";
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for(int i=1;i!=s.size();i++)
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out << s[i] << " ";
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out << "\""<< endl;
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}
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}
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else
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out << "@ yaxis label " << "\"" << s[3] << "\""<< endl;
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int length=data.size();
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if (!s[1].compare("cross")) length/=2;
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// Storing data in file "temp" as asked (series or parallel)
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for(int i=0;i!=length;i++) {
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switch (style) {
|
||||
case 1: { // Series Case
|
||||
if (s[1].compare("cross")) { // This is executed if not cross
|
||||
out << s1 << plotiterator << s2 << "\""<< data[i].property << "\"" << endl;
|
||||
out << s1 << plotiterator << s3 << "\""<< data[i].property << "\"" << endl;
|
||||
}
|
||||
else
|
||||
{
|
||||
out << s1 << plotiterator << s2 << "\""<< data[i+half_data].property << " vs " << data[i].property << "\"" << endl;
|
||||
out << s1 << plotiterator << s3 << "\""<< data[i+half_data].property << " vs " << data[i].property << "\"" << endl;
|
||||
}
|
||||
out << s1 << plotiterator << " symbol 1" << endl;
|
||||
out << s1 << plotiterator << " symbol size 0.50000" << endl;
|
||||
out << s1 << plotiterator << " symbol color 1" << endl;
|
||||
out << s1 << plotiterator << " symbol pattern 1" << endl;
|
||||
out << s1 << plotiterator << " symbol fill color "<< plotiterator+1 << endl;
|
||||
out << s1 << plotiterator << " symbol fill pattern 1" << endl;
|
||||
out << s1 << plotiterator << " symbol linewidth 1.0" << endl;
|
||||
out << s1 << plotiterator << " symbol linestyle 1" << endl;
|
||||
out << s1 << plotiterator << " symbol char 65" << endl;
|
||||
out << s1 << plotiterator << " symbol char font 0" << endl;
|
||||
plotiterator++;
|
||||
for(int j=0;j!=data[i].value.size(); j++)
|
||||
if (s[1].compare("cross"))
|
||||
out << data[i].value[j] << endl; // This is executed if not cross
|
||||
else
|
||||
out << data[i].value[j] << " " << data[i+half_data].value[j]<< endl; // This is executed if cross
|
||||
out << "&" << endl;
|
||||
break;
|
||||
}
|
||||
|
||||
case 2: { // Parallel Case
|
||||
if (s[1].compare("cross")) {
|
||||
out << s1 << plotiterator << s2 << "\""<< data[i].property << ": " << data[i].filename << "\"" << endl;
|
||||
if (s.size()<=2)
|
||||
out << s1 << plotiterator << s3 << "\"" << data[i].filename << "\"" << endl;
|
||||
else
|
||||
out << s1 << plotiterator << s3 << "\""<< data[i].property << ": " << data[i].filename << "\"" << endl;
|
||||
}
|
||||
else {
|
||||
out << s1 << plotiterator << s2 << "\""<< data[i+half_data].property << " vs " << data[i].property << ": " << data[i].filename << "\"" << endl;
|
||||
out << s1 << plotiterator << s3 << "\""<< data[i+half_data].property << " vs " << data[i].property << ": " << data[i].filename << "\"" << endl;
|
||||
}
|
||||
out << s1 << plotiterator << " symbol 0" << endl;
|
||||
out << s1 << plotiterator << " symbol size 0.50000" << endl;
|
||||
out << s1 << plotiterator << " symbol color 1" << endl;
|
||||
out << s1 << plotiterator << " symbol pattern 1" << endl;
|
||||
out << s1 << plotiterator << " symbol fill color "<< plotiterator+1 << endl;
|
||||
out << s1 << plotiterator << " symbol fill pattern 1" << endl;
|
||||
out << s1 << plotiterator << " symbol linewidth 1.0" << endl;
|
||||
out << s1 << plotiterator << " symbol linestyle 1" << endl;
|
||||
out << s1 << plotiterator << " symbol char 65" << endl;
|
||||
out << s1 << plotiterator << " symbol char font 0" << endl;
|
||||
plotiterator++;
|
||||
for(int j=0;j!=data[i].value.size(); j++)
|
||||
if (s[1].compare("cross")) {
|
||||
out << data[i].value[j] << endl; // This is executed if not cross
|
||||
}
|
||||
else
|
||||
out << data[i].value[j] << " " << data[i+half_data].value[j]<< endl; // This is executed if cross
|
||||
out << "&" << endl;
|
||||
break;
|
||||
}
|
||||
}
|
||||
}
|
||||
int rv=system("xmgrace temp &");
|
||||
}
|
||||
void plot_xmgrace_cross(sentence s, vector <fd> data) {
|
||||
ofstream out("temp");
|
||||
// Some string definitions
|
||||
string s1 = "@ s";
|
||||
string s2 = " comment ";
|
||||
string s3 = " legend ";
|
||||
int plotiterator=0; int set; int style;
|
||||
int half_data=data.size()/2;
|
||||
// Printing out X and Y axis properties
|
||||
out << "@ xaxis label char size 1.500000\n";
|
||||
out << "@ xaxis ticklabel char size 1.250000\n";
|
||||
out << "@ xaxis label " << "\"" << s[2] << "\""<< endl;
|
||||
out << "@ yaxis label char size 1.500000\n";
|
||||
out << "@ yaxis ticklabel char size 1.250000\n";
|
||||
out << "@ yaxis label " << "\"" << s[3] << "\""<< endl;
|
||||
|
||||
// Printing out legend properties
|
||||
out << "@ legend box linestyle 0\n";
|
||||
out << "@ legend 0.25, 0.8\n";
|
||||
|
||||
// Selecting style for series or parallel plotting.
|
||||
if (!s[0].compare("s")) style=1; else style=2;
|
||||
|
||||
// Storing data in file "temp" as asked (series or parallel)
|
||||
for(int i=0;i!=data.size()/2;i++) {
|
||||
switch (style) {
|
||||
case 1: { // Series Case
|
||||
out << s1 << plotiterator << s2 << "\""<< data[i+half_data].property << " vs " << data[i].property << "\"" << endl;
|
||||
out << s1 << plotiterator << s3 << "\""<< data[i+half_data].property << " vs " << data[i].property << "\"" << endl;
|
||||
out << s1 << plotiterator << " symbol 1" << endl;
|
||||
out << s1 << plotiterator << " symbol size 0.50000" << endl;
|
||||
out << s1 << plotiterator << " symbol color 1" << endl;
|
||||
out << s1 << plotiterator << " symbol pattern 1" << endl;
|
||||
out << s1 << plotiterator << " symbol fill color "<< plotiterator+1 << endl;
|
||||
out << s1 << plotiterator << " symbol fill pattern 1" << endl;
|
||||
out << s1 << plotiterator << " symbol linewidth 1.0" << endl;
|
||||
out << s1 << plotiterator << " symbol linestyle 1" << endl;
|
||||
out << s1 << plotiterator << " symbol char 65" << endl;
|
||||
out << s1 << plotiterator << " symbol char font 0" << endl;
|
||||
plotiterator++;
|
||||
for(int j=0;j!=data[i].value.size(); j++)
|
||||
out << data[i].value[j] << " " << data[i+half_data].value[j]<< endl;
|
||||
out << "&" << endl;
|
||||
break;
|
||||
}
|
||||
|
||||
case 2: { // Parallel Case
|
||||
out << s1 << plotiterator << s2 << "\""<< data[i+half_data].property << " vs " << data[i].property << ": " << data[i].filename << "\"" << endl;
|
||||
out << s1 << plotiterator << s3 << "\""<< data[i+half_data].property << " vs " << data[i].property << ": " << data[i].filename << "\"" << endl;
|
||||
out << s1 << plotiterator << " symbol 1" << endl;
|
||||
out << s1 << plotiterator << " symbol size 0.50000" << endl;
|
||||
out << s1 << plotiterator << " symbol color 1" << endl;
|
||||
out << s1 << plotiterator << " symbol pattern 1" << endl;
|
||||
out << s1 << plotiterator << " symbol fill color "<< plotiterator+1 << endl;
|
||||
out << s1 << plotiterator << " symbol fill pattern 1" << endl;
|
||||
out << s1 << plotiterator << " symbol linewidth 1.0" << endl;
|
||||
out << s1 << plotiterator << " symbol linestyle 1" << endl;
|
||||
out << s1 << plotiterator << " symbol char 65" << endl;
|
||||
out << s1 << plotiterator << " symbol char font 0" << endl;
|
||||
plotiterator++;
|
||||
|
||||
for(int j=0;j!=data[i].value.size(); j++)
|
||||
out << data[i].value[j] << " " << data[i+half_data].value[j]<< endl;
|
||||
out << "&" << endl;
|
||||
break;
|
||||
}
|
||||
}
|
||||
}
|
||||
int rv=system("xmgrace temp &");
|
||||
}
|
||||
|
||||
vector<fd> convert_to_float(sentence s, map<string, vector<int> > x, sentence sf) {
|
||||
vector<fd> datatemp;
|
||||
int style,set;
|
||||
|
||||
if (!s[0].compare("s")) style=1; else style=2;
|
||||
for(int i=1;i!=s.size();i++) {
|
||||
fd temp;
|
||||
switch (style) {
|
||||
case 1: { // This is series case
|
||||
set=0;
|
||||
for(int j=0;j!=f.size(); j++) {
|
||||
if (x[s[i]][j]) {
|
||||
if (!set) {
|
||||
temp.filename="Allfiles";
|
||||
temp.property=s[i];
|
||||
set=1;
|
||||
}
|
||||
for(int tt=1;tt!=f[j].size();tt++) {
|
||||
float t=atof(&f[j][tt][x[s[i]][j]][0]);
|
||||
temp.value.push_back(t);
|
||||
}
|
||||
}
|
||||
// datatemp.push_back(temp);
|
||||
}
|
||||
datatemp.push_back(temp);
|
||||
break;
|
||||
}
|
||||
case 2: { // This is parallel case.
|
||||
for(int j=0;j!=f.size(); j++) {
|
||||
if (x[s[i]][j]) {
|
||||
temp.filename=sf[j];
|
||||
temp.property=s[i];
|
||||
temp.value.clear();
|
||||
for(int tt=1;tt!=f[j].size();tt++) {
|
||||
float t= 0.0;
|
||||
if ((f[j][tt][x[s[i]][j]].compare("nan")))
|
||||
t = atof(&f[j][tt][x[s[i]][j]][0]);
|
||||
temp.value.push_back(t);
|
||||
}
|
||||
datatemp.push_back(temp);
|
||||
}
|
||||
else if (!s[i].compare("Step")) {
|
||||
temp.filename=sf[j];
|
||||
temp.property=s[i];
|
||||
temp.value.clear();
|
||||
for(int tt=1;tt!=f[j].size();tt++) {
|
||||
float t=atof(&f[j][tt][x[s[i]][j]][0]);
|
||||
temp.value.push_back(t);
|
||||
}
|
||||
datatemp.push_back(temp);
|
||||
}
|
||||
}
|
||||
break;
|
||||
}
|
||||
}
|
||||
}
|
||||
return datatemp;
|
||||
}
|
||||
|
||||
void do_averageall(vector<fd> x,int start,int end) {
|
||||
for(int i=0;i!=x.size();i++) {
|
||||
double average=0;
|
||||
double stdev=0;
|
||||
int finish;
|
||||
if (end==0)
|
||||
finish=x[i].value.size();
|
||||
else
|
||||
finish=end;
|
||||
|
||||
for (int j=start;j!=finish;j++)
|
||||
average+=x[i].value[j];
|
||||
average/=(double)(finish-start);
|
||||
for (int j=start;j!=finish;j++)
|
||||
stdev+=pow((x[i].value[j]-average),2);
|
||||
stdev/=(double)(finish-1-start);
|
||||
stdev=sqrt(stdev);
|
||||
cout << x[i].filename << ": " << x[i].property << "--- " << average << " " << stdev << " " << start << " " << finish << " Total Size " << x[i].value.size() << endl;
|
||||
}
|
||||
}
|
||||
|
||||
void do_averagesingle(vector<fd> x,int start,int end, string str) {
|
||||
for(int i=0;i!=x.size();i++) {
|
||||
if (!x[i].filename.compare(str)) {
|
||||
float average=0;
|
||||
float stdev=0;
|
||||
int finish;
|
||||
if (end==0) finish=x[i].value.size();
|
||||
for (int j=start;j!=finish;j++)
|
||||
average+=x[i].value[j];
|
||||
average/=(double)(finish-start);
|
||||
for (int j=start;j!=finish;j++)
|
||||
stdev+=pow((x[i].value[j]-average),2);
|
||||
stdev/=(double)(finish-1-start);
|
||||
stdev=sqrt(stdev);
|
||||
cout << x[i].filename << ": " << x[i].property << "--- " << average << " " << stdev << " " << start << " " << finish << endl;
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
void do_scale_single(vector<fd> &x,float factor, string filename, string property) {
|
||||
for(int i=0;i!=x.size();i++)
|
||||
if ((!x[i].filename.compare(filename)) && (!x[i].property.compare(property))) {
|
||||
fd temp;
|
||||
temp.filename=filename;
|
||||
temp.property=property+".scl";
|
||||
for (int j=0;j!=x[i].value.size();j++)
|
||||
temp.value.push_back(x[i].value[j]*factor);
|
||||
x.push_back(temp);
|
||||
}
|
||||
}
|
||||
|
||||
void do_inverse_single(vector<fd> &x, string filename, string property) {
|
||||
for(int i=0;i!=x.size();i++)
|
||||
if ((!x[i].filename.compare(filename)) && (!x[i].property.compare(property))) {
|
||||
fd temp;
|
||||
temp.filename=filename;
|
||||
temp.property=property+".inv";
|
||||
for (int j=0;j!=x[i].value.size();j++)
|
||||
temp.value.push_back(1.0/x[i].value[j]);
|
||||
x.push_back(temp);
|
||||
}
|
||||
}
|
||||
|
||||
void do_write_data(vector<fd> x, sentence line) {
|
||||
// int startvalue,endvalue;
|
||||
// if (!line_data[1].compare("start")) startvalue=0; else startvalue=atoi(&line_data[2][0]);
|
||||
// if (!line_data[2].compare("end")) endvalue=0; else endvalue=atoi(&line_data[3][0]);
|
||||
// for(int j=3;j!=line.size();j++)
|
||||
// for(int i=0;i!=x.size();i++)
|
||||
// if (!x[i].property.compare(line[i])) {
|
||||
// // Create a filename
|
||||
// // open a file.
|
||||
// // Write the data
|
||||
// }
|
||||
}
|
||||
|
||||
void do_subtract(vector<fd>& x, sentence line) {
|
||||
int indexfile1=-1;
|
||||
int indexfile2=-1;
|
||||
int minlength;
|
||||
for(int i=0;i!=x.size();i++)
|
||||
if ((!x[i].property.compare(line[1])) && (!x[i].filename.compare(line[3])))
|
||||
indexfile1=i;
|
||||
for(int i=0;i!=x.size();i++)
|
||||
if ((!x[i].property.compare(line[2])) && (!x[i].filename.compare(line[3])))
|
||||
indexfile2=i;
|
||||
if ((indexfile1>=0) && (indexfile2>=0)) {
|
||||
fd temp;
|
||||
temp.property=line[4];
|
||||
temp.filename=line[3];
|
||||
if (x[indexfile1].value.size()<x[indexfile2].value.size())
|
||||
minlength=x[indexfile1].value.size();
|
||||
else
|
||||
minlength=x[indexfile2].value.size();
|
||||
|
||||
for (int j=0;j!=minlength;j++)
|
||||
temp.value.push_back(x[indexfile1].value[j]-x[indexfile2].value[j]);
|
||||
x.push_back(temp);
|
||||
}
|
||||
}
|
||||
|
||||
void do_add(vector<fd>& x, sentence line) {
|
||||
fd temp;
|
||||
int length=line.size();
|
||||
temp.property=line[length-1];
|
||||
temp.filename=line[length-2];
|
||||
vector <int> index;
|
||||
int minlength=10000000;
|
||||
|
||||
for(int i=0;i!=length-3;i++)
|
||||
index.push_back(-1);
|
||||
for(int j=1;j!=length-2;j++)
|
||||
for(int i=0;i!=x.size();i++)
|
||||
if ((!x[i].property.compare(line[j])) && (!x[i].filename.compare(line[length-2])))
|
||||
index[j-1]=i;
|
||||
|
||||
for(int i=0;i!=length-3;i++) {
|
||||
if (index[i]>-1)
|
||||
if (minlength>x[index[i]].value.size())
|
||||
minlength=x[index[i]].value.size();
|
||||
}
|
||||
|
||||
for (int j=0;j!=minlength;j++) {
|
||||
float value=0;
|
||||
for (int i=0;i!=length-2;i++)
|
||||
if (index[i]>0)
|
||||
value+=x[index[i]].value[j];
|
||||
temp.value.push_back(value);
|
||||
}
|
||||
x.push_back(temp);
|
||||
}
|
||||
|
||||
void do_analysis(vector<fd> &data,string file) {
|
||||
ifstream inp_anal(file.c_str());
|
||||
if (inp_anal) {
|
||||
string line;
|
||||
while(getline(inp_anal,line)) {
|
||||
sentence line_data=split(line);
|
||||
|
||||
// Average
|
||||
if (!line_data[0].compare("average")) {
|
||||
int startvalue,endvalue;
|
||||
if (!line_data[2].compare("start")) startvalue=0; else startvalue=atoi(&line_data[2][0]);
|
||||
if (!line_data[3].compare("end")) endvalue=0; else endvalue=atoi(&line_data[3][0]);
|
||||
if (!line_data[1].compare("all"))
|
||||
do_averageall(data,startvalue,endvalue);
|
||||
else
|
||||
do_averagesingle(data,startvalue,endvalue,line_data[1]);
|
||||
}
|
||||
|
||||
// Scale
|
||||
if (!line_data[0].compare("scale")) {
|
||||
float factor=atof(&line_data[3][0]);
|
||||
do_scale_single(data,factor,line_data[1],line_data[2]);
|
||||
}
|
||||
|
||||
// Inverse
|
||||
if (!line_data[0].compare("inverse"))
|
||||
do_inverse_single(data,line_data[1],line_data[2]);
|
||||
|
||||
// Write Data
|
||||
if (!line_data[0].compare("write"))
|
||||
do_write_data(data,line_data);
|
||||
|
||||
// Add : Think about it and write
|
||||
if (!line_data[0].compare("write")) {
|
||||
do_add(data,line_data);
|
||||
}
|
||||
// Subtract : Think about it and write
|
||||
if (!line_data[0].compare("subtract")) {
|
||||
cout << "coming here" << endl;
|
||||
do_subtract(data,line_data);
|
||||
}
|
||||
|
||||
if (!line_data[0].compare("graph")) {
|
||||
}
|
||||
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
void print_start() {
|
||||
int rv=system("clear ");
|
||||
cout << endl;
|
||||
cout << "Files Read: --- " << endl;
|
||||
}
|
||||
|
||||
int main (int argc, char **argv) {
|
||||
sentence s;
|
||||
sentence stringfile;
|
||||
string anal_file="";
|
||||
vector <fd> data;
|
||||
map<string, vector<int> > inp_index;
|
||||
print_start();
|
||||
read_input(argc,argv,stringfile,anal_file); // Read the input file
|
||||
s=get_userinput(); // Read the parameters
|
||||
transform_userinput(s); // Transform the parameters to correct names
|
||||
inp_index=update2_userinput(s); // Assign indices
|
||||
print_file_index_output(s,inp_index,stringfile); // Print file index information
|
||||
data=convert_to_float(s,inp_index,stringfile); // Convert the stored data in float formation
|
||||
if (anal_file.size())
|
||||
do_analysis(data,anal_file); // Do analysis if wanted.
|
||||
plot_xmgrace(s,data); // Plot the data in xmgrace
|
||||
return 0;
|
||||
}
|
||||
Binary file not shown.
|
|
@ -0,0 +1,7 @@
|
|||
# This 1-liner will extract all lines from
|
||||
# the 3rd run in a log file and plot
|
||||
# column 8 against column 1
|
||||
#
|
||||
# By Karl Hammond karlh at ugcs.caltech.edu
|
||||
|
||||
awk '/Step/ {n++} /Step/,/step/ {if (n==3) print}' log.lammps | grep -iv step | xmgrace -block - -bxy 1:8
|
||||
|
|
@ -0,0 +1,6 @@
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|||
# This 1-liner will extract up to a billion lines from
|
||||
# a simple log file and plot all the columns
|
||||
#
|
||||
# by Aidan Thompson athomps at sandia.gov
|
||||
|
||||
grep -A1000000000 Step log.lammps | grep -v Step | xmgrace -nxy -
|
||||
|
|
@ -0,0 +1,18 @@
|
|||
#!/sw/bin/awk -f
|
||||
|
||||
# Usage: ./plotthermodata.awk log.lammps | xmgrace -nxy -
|
||||
|
||||
BEGIN {
|
||||
if ( stepnum == 0 ) stepnum = 1 # if unset, pick first set of output
|
||||
print "@xaxis label \"Time Step\""
|
||||
}
|
||||
/Step/ {
|
||||
num += 1
|
||||
if ( num != stepnum ) next
|
||||
n = 0
|
||||
for (i=2; i<=NF; i++) {
|
||||
print "@s" n, "legend \"" $i "\""
|
||||
n += 1
|
||||
}
|
||||
}
|
||||
/Step/,/step/ { if ( $0 ~ /[sS]tep/ ) next; else print }
|
||||
Loading…
Reference in New Issue