lammpsplot.cpp
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Created: Sun, Aug 11, 00:45

lammpsplot.cpp
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	// By Vikas Varshney @ vv0210 at gmail dot com

	#include <stdlib.h>
	#include <iostream>
	#include <fstream>
	#include <string>
	#include <vector>
	#include <cstring>
	#include <cctype>
	#include <cstdlib>
	#include <map>
	#include <iomanip>
	#include <algorithm>
	#include <cmath>

	using namespace std;

	typedef vector<string> sentence;
	typedef vector<sentence> filedata;
	typedef string::size_type s_type;

	vector<filedata> f;

	class fd {
	public:
	string filename;
	string property;
	vector <float> value;
	};


	/* This function splits the sentence into array of strings seperated by " "*/
	sentence split(const string& s) {
	sentence a;
	s_type i=0;
	while (i!=s.size()) {
	while (i!=s.size() && isspace(s[i])) {
	++i;
	}

	s_type j=i;
	while (j!=s.size() && !isspace(s[j]))
	++j;

	if (i!=j) {
	a.push_back(s.substr(i,j-i));
	i=j;
	}
	}
	return a;
	}

	/* This function add array of strings (passed as string) to a sentence */
	sentence add_strings(sentence& temp_entry, const string l) {
	sentence temp=split(l);
	s_type mm;
	if (temp.size()!=0)
	for (mm=0;mm!=temp.size();mm++)
	temp_entry.push_back(temp[mm]);
	else
	return temp_entry;
	return temp_entry;
	}

	/* This function reads the logfile produced by lammps */
	void readlogfile_multi(filedata& atemp, ifstream& input, int leave_index) {
	const string ll("----------------");
	const string step("Step");
	const string Mem("Memory");
	const string Loop("Loop");
	int leave=0;
	string line;
	s_type kk=0,mm,kkk;
	s_type length;
	int style;
	int halffile=0;
	while (getline(input,line)) {
	sentence entry=split(line);
	if (entry.size()!=0)
	// Find keyword Memory
	if (!entry[0].compare(Mem)) {
	getline(input,line);
	entry=split(line);
	// Style = 1 means multi line format and style = 2 means single line format
	if (!entry[0].compare(ll)) style=1; else if (!entry[0].compare(step)) style=2; else cout << "style not matching" << endl;
	switch (style) {
	case 1: {
	// Read the line till ll comes up next and store it in a variable.
	sentence zero;
	sentence one;

	zero.push_back(entry[1]);
	one.push_back(entry[2]);
	getline(input,line);
	entry=split(line);
	do {
	if (entry.size()!=0)
	for(int i=0;i<entry.size();i+=3) {
	zero.push_back(entry[i]);
	one.push_back(entry[i+2]);
	}
	getline(input,line);
	entry=split(line);
	if (!entry[0].compare(Loop))
	break;
	}
	while (entry[0].compare(ll));
	if (!atemp.size())
	atemp.push_back(zero);
	atemp.push_back(one);
	int length=zero.size();
	int t=0;

	// Read all the lines till Loop comes up.
	while (entry[0].compare(Loop)) {
	t++;
	sentence a1;
	a1.push_back(entry[2]);
	for(int j=0;j<(length+1)/3;j++) {
	if (!getline(input,line)) {
	halffile=1;
	break;
	}
	entry=split(line);
	for(int i=0;i<entry.size();i+=3)
	a1.push_back(entry[i+2]);
	}
	if (a1.size()==length)
	atemp.push_back(a1);
	if (halffile)
	break;
	if (!getline(input,line))
	break;
	else
	entry=split(line);
	}
	break;
	}
	case 2:
	{
	sentence zero;
	for(int i=0;i!=entry.size();i++)
	zero.push_back(entry[i]);
	getline(input,line);
	entry=split(line);
	if (!atemp.size())
	atemp.push_back(zero);
	int length=zero.size();
	while(entry[0].compare(Loop)) {
	sentence a1;
	for(int i=0;i!=entry.size();i++)
	a1.push_back(entry[i]);
	atemp.push_back(a1);
	getline(input,line);
	entry=split(line);
	if (entry.size()<length) break;
	}
	break;
	}
	}

	if (leave_index>leave) {
	atemp.clear();
	leave++;
	}
	}
	}
	}

	/* This function1 searches for a string in a sentence and return true/false*/
	bool search_string(string str, sentence sen, int& j) {
	j=0;
	while (j!=sen.size()) {
	if (!sen[j].compare(str)) {
	break;
	}
	j++;
	}
	if (j==sen.size()) return false; else return true;
	}

	/* This function is used to ask user to input parameters to be plotted*/
	sentence get_userinput() {
	string temp;
	sentence t;
	cout << "Enter the parameter(s) of which you want the plot for files, read successfully:" << endl;
	getline(cin,temp);
	t=split(temp);
	if (!t[1].compare("cross"))
	if (t.size()!=4) {
	cout << "Currently only two cross parameters can be plotted \nThe syntax is s/p cross param1 param2\n" << endl;
	exit(1);
	}
	return t;
	}

	/This function replaces certain input keywords to their appropriate words found in lammps file/
	void transform_userinput(sentence& temp) {
	if (temp.size()) {
	for(int i=1;i!=temp.size();i++) {
	if (!temp[i].compare("t")) temp[i].replace(0,temp[i].length(),"Temp");
	if (!temp[i].compare("p")) temp[i].replace(0,temp[i].length(),"Press");
	if (!temp[i].compare("v")) temp[i].replace(0,temp[i].length(),"Volume");
	if (!temp[i].compare("vd")) temp[i].replace(0,temp[i].length(),"E_vdwl");
	if (!temp[i].compare("te")) temp[i].replace(0,temp[i].length(),"TotEng");
	if (!temp[i].compare("ke")) temp[i].replace(0,temp[i].length(),"KinEng");
	if (!temp[i].compare("pe")) temp[i].replace(0,temp[i].length(),"PotEng");
	if (!temp[i].compare("be")) temp[i].replace(0,temp[i].length(),"E_bond");
	if (!temp[i].compare("ae")) temp[i].replace(0,temp[i].length(),"E_angle");
	if (!temp[i].compare("de")) temp[i].replace(0,temp[i].length(),"E_dihed");
	if (!temp[i].compare("ce")) temp[i].replace(0,temp[i].length(),"E_coul");
	if (!temp[i].compare("le")) temp[i].replace(0,temp[i].length(),"E_long");
	}
	}
	}

	/* This function searches if the parameter is present in the lammps file and return a array of
	associated with the parameter stored in string */
	map<string, vector<int> > update2_userinput(sentence temp) {
	if ((!temp[0].compare("s")) \|\| (!temp[0].compare("p"))) {
	s_type j;
	int jtemp;
	int notfind;
	int notfindall=1;
	map<string, vector<int> > ret;
	sentence::iterator tb=temp.begin();
	for(j=0;j!=f.size();j++)
	ret[*tb].push_back(0);
	tb++;

	for(sentence::iterator aa=tb; aa!=temp.end(); aa++) {
	notfind=1;
	for(j=0;j!=f.size();j++) {
	if (search_string(*aa,f[j][0],jtemp)) {
	ret[*aa].push_back(jtemp);
	notfind=0;
	notfindall=0;
	}
	else
	ret[*aa].push_back(0);
	}
	if (notfind) {
	temp.erase(aa);
	aa--;
	}
	}

	if (notfindall) {
	cerr << "\nDid not find any matching parameters in any input files, read successfully. Please check!!!\n\n";
	exit(1);
	}
	return ret;
	}
	else {
	cerr << "\nFirst string should be s (for series) or p (for parallel)\n\n" << endl;
	exit(1);
	}
	}

	/* This function just print out a line with string str on standard output*/
	void print_line(string str) {
	for(int i=0;i<100;i++)
	cout << str;
	cout << endl;
	}

	/This function reads the data from the input files/
	void read_input(int argc, char** argv, sentence& sf,string& analysisfile) {
	filedata a;
	int success_filecounter=0;
	int leave_index=0;
	// Read the data into the file.
	for (int i=1; i<argc; ++i) {
	if (!strcmp(argv[i],"-leave")) {
	leave_index=atoi(argv[i+1]);
	i++;
	continue;
	}

	if (!strcmp(argv[i],"-analysis")) {
	analysisfile=argv[i+1];
	i++;
	continue;
	}

	ifstream in(argv[i]);
	if (in) {
	sf.push_back(argv[i]);
	cout << "Reading file : " << argv[i] << endl;
	if (a.size())
	a.clear();
	readlogfile_multi(a,in,leave_index);
	f.push_back(a);
	in.close();
	success_filecounter++;
	} else {
	cerr << "Cannot open file: " << argv[i] << endl;
	}
	}

	if(!success_filecounter)
	exit(1);
	else {
	sentence aa;
	int exists;
	cout << endl;
	cout << "Select parameters to plot from following: --- " << endl;
	for (int i=0;i<success_filecounter;i++) {
	for(int j=0;j<f[i][0].size();j++) {
	exists=0;
	for(int k=0;k!=aa.size();k++)
	if (!f[i][0][j].compare(aa[k])) {
	exists=1;
	break;
	}
	if (!exists)
	aa.push_back(f[i][0][j]);
	}
	}

	for(int k=0;k!=aa.size();k++) {
	if (!aa[k].compare("Temp")) aa[k].replace(0,aa[k].length(),"Temp(t)");
	if (!aa[k].compare("Press")) aa[k].replace(0,aa[k].length(),"Press(p)");
	if (!aa[k].compare("Volume")) aa[k].replace(0,aa[k].length(),"Volume(v)");
	if (!aa[k].compare("E_vdwl")) aa[k].replace(0,aa[k].length(),"E_vdwl(vd)");
	if (!aa[k].compare("TotEng")) aa[k].replace(0,aa[k].length(),"TotEng(te)");
	if (!aa[k].compare("KinEng")) aa[k].replace(0,aa[k].length(),"KinEng(ke)");
	if (!aa[k].compare("PotEng")) aa[k].replace(0,aa[k].length(),"PotEng(pe)");
	if (!aa[k].compare("E_bond")) aa[k].replace(0,aa[k].length(),"E_bond(be)");
	if (!aa[k].compare("E_angle")) aa[k].replace(0,aa[k].length(),"E_angle(ae)");
	if (!aa[k].compare("E_dihed")) aa[k].replace(0,aa[k].length(),"E_dihed(de)");
	if (!aa[k].compare("E_coul")) aa[k].replace(0,aa[k].length(),"E_coul(ce)");
	if (!aa[k].compare("E_long")) aa[k].replace(0,aa[k].length(),"E_long(le)");
	cout << aa[k];
	if (aa[k].size()<8) cout << "\t";
	cout << "\t";
	if (k%6==5) cout << endl;
	}
	cout << "\n--------------\n\n";
	cout << "Please enter your parameters in the following format: --- " << endl;
	cout << "1. First string should be 'p' or 's' for plotting parameters from different files in parallel or series" << endl;
	cout << "2. Please enter one or more parameters listed above after entering the first string." << endl;
	cout << "3. For certain parameters, short forms may be used as listed in bracket above" << endl;
	cout << " ----- Example: To plot total energy, please type 'p te'." << endl;
	cout << "4. In order to plot one parameter with respect to other, please type 'cross' after p/s followed by two parameters" << endl;
	cout << "5. The independent parameter could be 'Step' as mentioned above." << endl;
	cout << "6. Currently, only two parameters can be plotted with respect to each other." << endl;
	cout << " ----- Example: To plot temperature vs. pressure p cross t p" << endl ;
	cout << "--------------\n\n";
	cout << "For analysis, please exit and use -analysis flag with filename. The file should contain atleast one of these commands: --- " << endl;
	cout << "1. average all/single_filename startvalue(start) endvalue(end)" << endl;
	cout << "2. scale filename property factor" << endl;
	cout << "3. inverse filename property" << endl;
	cout << "4. write Under Coding" << endl;
	cout << "5. subtract property1 property2 filename outputpropertyname" << endl;
	cout << "6. add Under Coding" << endl;
	cout << "--------------\n\n";
	}
	}

	string print_space(int t) {
	string f;
	for (int i=0;i!=t;i++)
	f.push_back(' ');
	return f;
	}


	/This function prints out the parameter associated index in successfully read file /
	void print_file_index_output(sentence s, map<string, vector<int> > x, sentence sf) {
	size_t maxlen=0;
	for(int i=0;i!=sf.size();i++)
	maxlen=max(maxlen,sf[i].length());
	cout << print_space(maxlen+11);
	for(sentence::iterator aa=++s.begin(); aa!=s.end(); aa++)
	cout << *aa << "\t";
	cout << endl;

	for(int j=0;j!=f.size();j++) {
	cout << "File-> " << sf[j] << print_space(maxlen-sf[j].length()+1) <<": ";
	for(sentence::iterator aa=++s.begin(); aa!=s.end(); aa++) {
	cout << x[*aa][j] << "\t";
	}
	cout << endl;
	}
	}

	void plot_xmgrace(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";
	if (s[1].compare("cross"))
	out << "@ xaxis label " << "\"time\""<< endl;
	else
	out << "@ xaxis label " << "\"" << s[2] << "\""<< endl;
	out << "@ yaxis label char size 1.500000\n";
	out << "@ yaxis ticklabel char size 1.250000\n";

	// 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;

	if (s[1].compare("cross")) {
	if (s.size()==2) {
	out << "@ yaxis label " << "\"";
	for(int i=1;i!=s.size();i++)
	out << s[i] << " ";
	out << "\""<< endl;
	}
	}
	else
	out << "@ yaxis label " << "\"" << s[3] << "\""<< endl;
	int length=data.size();
	if (!s[1].compare("cross")) length/=2;
	// Storing data in file "temp" as asked (series or parallel)
	for(int i=0;i!=length;i++) {
	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;
	}

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