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defor_monoclinic_struct.cpp
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#include <iostream>
#include <fstream>
#include <sstream>
#include <stdlib.h>
#include <iomanip>
#include <stdio.h>
#include <string>
#include <cmath>
#include <vector>
#include <algorithm>
#include <iterator>
using namespace std;
#define _USE_MATH_DEFINES
/*
**********************************DOCUMENTATION******************************
* Author: ASIF IQBAL BHATTI
* DATE : 24/10/2015
* VERSION: 1.0
* USAGE: icpc/icc/g++ -O3 defor.cpp (Intel/gcc compiler) tested.
* PURPOSE: Generating the deformed structures along each lattice vector
* ONLY for Monoclinic structure
* Reads only a POSCAR (VASP) file.
*****************************END OF DOCUMENTATION****************************
*/
template <class T>
bool from_string(T& t, const std::string& s, std::ios_base& (*f)(std::ios_base&))
{
std::istringstream iss(s);
return !(iss >> f >> t).fail();
}
int main()
{
int array_size = 100000;
int arr = 3;
float a, b, l, ch, j, alpha, beta, gamma, fact, scale;
float h1[3]={}, v1[3]={}, r1[3]={};
float x, y, z, vol, cons, atnum;
float latvec[arr][arr], xx;
char vectors[4] = "xyz";
char select;
int loop = 0, loop2;
string array[array_size];
string adjust_vec;
FILE * outputfile;
std::cout.precision(12);
std::ifstream indata;
string filename;
std::string line, coord;
cout << "\n" << endl;
cout << std::string(30, '-') << "\033[1;31m PROGRAM USAGE \033[0m" << std::string(30, '-') << endl;
cout << endl;
cout << " [*] Deform volume keeping a:b:c ratio constant." << endl;
cout << " [*] Vary lattice vector along each direction." << endl;
cout << " [*] Vary lattice while volume fixed." << "\n" << endl;
std::cout << std::string(75, '-') << endl;
cout << "\033[1;32m ENTERING THE PROGRAM... \033[0m" << endl;
cout << " | Enter the POSCAR filename : ";
getline(cin, filename);
indata.open(filename.c_str(), ios::in);
if (indata.is_open()){
cout << " | File opened succesfully: \n";
cout << " | Reading ... ";
while (! indata.eof() )
{
getline (indata,line);
// cout << line << endl;
array[loop]=line;
loop++;
}
cout <<"# of lines detected: " << loop << endl;
std::cout << std::string(60, '-') << std::endl;
indata.close();
}
else if(!indata.is_open())
{
cout << " Unable to open file" << endl;
exit(0);
}
cout << "The title of the file is: \t" << array[0] <<endl;
cout << "The scaling factor is: \t" << array[1] <<endl;
for (loop2=2; loop2<5;loop2++) {
int i = loop2 - 1, j = 1;
stringstream iss(array[loop2]);
string buf;
vector<string> tokens;
while (iss >> buf)
{
tokens.push_back(buf);
if(from_string<float>(xx, std::string(buf), std::dec))
{
latvec[i][j] = xx;
// printf("%16.12f\t", latvec[i][j]* ::atof(array[1].c_str()));
// cout << i << "\t" << j << endl;
j++;
}
}
std::cout << endl;
}
//*************************** Display output*******************************
for ( int k=1; k < 4; k++ ) {
for ( int p=1; p < 4; p++ ) {
printf("%16.12f\t", latvec[k][p]* ::atof(array[1].c_str()));
}
std::cout << endl;
}
cout << "\n"; cout << "Magnitude of latice vectors: " << "\n" << endl;
for ( int k=1; k < 4; k++ ) {
for ( int p=1; p < 4; p++ ) {
h1[k-1] = h1[k-1] + latvec[k][p]*latvec[k][p];
}
cout << " |" << vectors[k-1]<< "| = " << "\t"; std::cout << sqrt(h1[k-1]) << endl;
}
for (int k = 0; k < 3; k++) { h1[k]=sqrt(h1[k]);}
//***************************** Generating angles
alpha = acos ((latvec[2][1]*latvec[3][1]+latvec[2][2]*latvec[3][2]+latvec[2][3]*latvec[3][3])/(h1[1]*h1[2])) *180/M_PI;
printf("%4s %12.4f\n"," alpha:", alpha);
beta = acos ((latvec[1][1]*latvec[3][1]+latvec[1][2]*latvec[3][2]+latvec[1][3]*latvec[3][3])/(h1[0]*h1[2])) *180/M_PI;
printf("%4s %12.4f\n"," beta :", beta);
gamma = acos ((latvec[1][1]*latvec[2][1]+latvec[1][2]*latvec[2][2]+latvec[1][3]*latvec[2][3])/(h1[0]*h1[1])) *180/M_PI;
printf("%4s %12.4f\n"," gamma:", gamma);
printf("%4s %12.4f\n"," volume:", h1[0]*h1[1]*h1[2]*sin (beta*3.14/180) );
//
cout << "\nSECTION A: To calculate lattice vectors with a given volume." << endl;
cout << "This section concern with changing lattice constant if we were given volume." << endl;
cout << "If volume --> delta(a, b, c)." << "\n" << endl;
cout << "Enter yes or no to set lattice vectors: "; cin>>adjust_vec;
if (adjust_vec == "yes" or adjust_vec == "y" )
{
cout << " Enter volume of a crystal to set lattice vectors: " << "\t" << endl;cin>>vol;
// Apply over here the scaling law.
// (ratio of volume)^3 = (ratio of lengths)^3
fact = pow(vol/(h1[0]*h1[1]*h1[2]*sin (beta*3.14/180)),1.0/3.0);
for (int k=1; k < 4; k++) {
r1[k-1] = h1[k-1] * fact;
printf("%12.4f\n", r1[k-1]);
}
printf("%4s %12.4f\n"," volume of the final structure:", r1[0]*r1[1]*r1[2]*sin (beta*3.14/180) );
}
else if (adjust_vec == "no" or adjust_vec == "n" )
{ printf("Exiting from this section.");}
cout << "Select an option along which to deform the crystal ... " << "\n" << endl;
cout << "Type: " << "x" << " y " << " z " << " or volume (v)" << endl << flush; cin >> select;
cout << "Entered option is : " << "[" <<select << "]" << endl;
cout << "Number of strain values (odd) : "; cin>>b;
if ( b <= 0) std::cout << "Strain values must be a positive integer" << "\n";
cout << "Deformation value : "; std::cin >> a; cout <<"\n";
if (a < 0) a = abs(a);
//****************** Check to see if the value is real or not***********************************
while(std::cin.fail()) {
std::cout << "Not real number: " << std::endl;
std::cin.clear();
std::cin.ignore(256,'\n');
std::cin >> a;
}
ch = (2*a)/(b-1);
j = 0;
outputfile = fopen("deformationstruct.dat", "w");
switch(select)
{
case 'x':
case 'X':
fprintf(outputfile, "%10s %14s %14s\n","X", "Y", "Z");
fprintf(outputfile, " ");; for (int i=0; i < 52; i++) {fprintf(outputfile,"_");}; fprintf(outputfile, "\n");
for( int i = 0; i < b; i++ )
{
j = i * ch - a;
// printf("%4d %10.4f %16.10f\n", i, j, j*h1[0] + h1[0]);
fprintf(outputfile,"%16.10f %16.10f %16.10f\n", j*latvec[1][1] + latvec[1][1], j*latvec[1][2] + latvec[1][2], j*latvec[1][3] + latvec[1][3] );
fprintf(outputfile,"%16.10f %16.10f %16.10f\n", latvec[2][1], latvec[2][2], latvec[2][3] );
fprintf(outputfile,"%16.10f %16.10f %16.10f\n", latvec[3][1], latvec[3][2], latvec[3][3] );
if (int (b/2.0) == i) cout << " Original lattice vector from a file\n" << endl;
fprintf(outputfile, "\n");
printf("%16.10f %16.10f %16.10f\n", j*latvec[1][1] + latvec[1][1], j*latvec[1][2] + latvec[1][2], j*latvec[1][3] + latvec[1][3] );
printf("%16.10f %16.10f %16.10f\n", latvec[2][1], latvec[2][2], latvec[2][3] );
printf("%16.10f %16.10f %16.10f\n", latvec[3][1], latvec[3][2], latvec[3][3] );
v1[0] = pow(j*latvec[1][1] + latvec[1][1],2) + pow(j*latvec[1][2] + latvec[1][2],2) + pow(j*latvec[1][3] + latvec[1][3],2) ;
v1[1] = pow(latvec[2][1],2) + pow(latvec[2][2],2) + pow(latvec[2][3],2);
v1[2] = pow(latvec[3][1],2) + pow(latvec[3][2],2) + pow(latvec[3][3],2);
for (int k = 0; k < 3; k++) { v1[k]=sqrt(v1[k]);}
printf("%6s %12.4f\n"," volume:", v1[0]*v1[1]*v1[2]*sin (beta*3.14/180) );
printf("\n");
}
break;
case 'y':
case 'Y':
fprintf(outputfile, "%10s %14s %14s\n","X", "Y", "Z");
fprintf(outputfile, " ");; for (int i=0; i < 52; i++) {fprintf(outputfile,"_");}; fprintf(outputfile, "\n");
for( int i = 0; i < b; i++ )
{
j = i * ch - a;
// printf("%4d %10.4f %16.10f\n", i, j, j*h1[1] + h1[1]);
fprintf(outputfile,"%16.10f %16.10f %16.10f\n", latvec[1][1], latvec[1][2], latvec[1][3] );
fprintf(outputfile,"%16.10f %16.10f %16.10f\n", j*latvec[2][1] + latvec[2][1], j*latvec[2][2] + latvec[2][2], j*latvec[2][3] + latvec[2][3] );
fprintf(outputfile,"%16.10f %16.10f %16.10f\n", latvec[3][1], latvec[3][2], latvec[3][3] );
if (int (b/2.0) == i) cout << " Original lattice vector from a file\n" << endl;
fprintf(outputfile, "\n");
printf("%16.10f %16.10f %16.10f\n", latvec[1][1], latvec[1][2], latvec[1][3] );
printf("%16.10f %16.10f %16.10f\n", j*latvec[2][1] + latvec[2][1], j*latvec[2][2] + latvec[2][2], j*latvec[2][3] + latvec[2][3] );
printf("%16.10f %16.10f %16.10f\n", latvec[3][1], latvec[3][2], latvec[3][3] );
v1[0] = pow(latvec[1][1],2) + pow(latvec[1][2],2) + pow(latvec[1][3],2);
v1[1] = pow(j*latvec[2][1] + latvec[2][1],2) + pow(j*latvec[2][2] + latvec[2][2],2) + pow(j*latvec[2][3] + latvec[2][3],2);
v1[2] = pow(latvec[3][1],2) + pow(latvec[3][2],2) + pow(latvec[3][3],2);
for (int k = 0; k < 3; k++) { v1[k]=sqrt(v1[k]);}
printf("%6s %12.4f\n"," volume:", v1[0]*v1[1]*v1[2]*sin (beta*3.14/180) );
printf("\n");
}
break;
case 'z':
case 'Z':
fprintf(outputfile, "%10s %14s %14s\n","X", "Y", "Z");
fprintf(outputfile, " ");; for (int i=0; i < 52; i++) {fprintf(outputfile,"_");}; fprintf(outputfile, "\n");
for( int i = 0; i < b; i++ )
{
j = i * ch - a;
// printf("%4d %10.4f %16.10f\n", i, j, j*h1[2] + h1[2]);
fprintf(outputfile,"%16.10f %16.10f %16.10f\n", latvec[1][1], latvec[1][2], latvec[1][3] );
fprintf(outputfile,"%16.10f %16.10f %16.10f\n", latvec[2][1], latvec[2][2], latvec[2][3] );
fprintf(outputfile,"%16.10f %16.10f %16.10f\n", j*latvec[3][1] + latvec[3][1], j*latvec[3][2] + latvec[3][2], j*latvec[3][3] + latvec[3][3] );
if (int (b/2.0) == i) cout << " Original lattice vector from a file\n" << endl;
fprintf(outputfile, "\n");
printf("%16.10f %16.10f %16.10f\n", latvec[1][1], latvec[1][2], latvec[1][3] );
printf("%16.10f %16.10f %16.10f\n", latvec[2][1], latvec[2][2], latvec[2][3] );
printf("%16.10f %16.10f %16.10f\n", j*latvec[3][1] + latvec[3][1], j*latvec[3][2] + latvec[3][2], j*latvec[3][3] + latvec[3][3] );
v1[0] = pow(latvec[1][1],2) + pow(latvec[1][2],2) + pow(latvec[1][3],2);
v1[1] = pow(latvec[2][1],2) + pow(latvec[2][2],2) + pow(latvec[2][3],2);
v1[2] = pow(j*latvec[3][1] + latvec[3][1],2) + pow(j*latvec[3][2] + latvec[3][2],2) + pow(j*latvec[3][3] + latvec[3][3],2);
for (int k = 0; k < 3; k++) { v1[k]=sqrt(v1[k]);}
printf("%6s %12.4f\n"," volume:", v1[0]*v1[1]*v1[2]*sin (beta*3.14/180) );
printf("\n");
}
break;
case 'v':
case 'V':
fprintf(outputfile, "%10s %14s %14s\n","X", "Y", "Z");
fprintf(outputfile, " ");; for (int i=0; i < 52; i++) {fprintf(outputfile,"_");}; fprintf(outputfile, "\n");
for( int i = 0; i < b; i++ )
{
j = i * ch - a;
fprintf(outputfile,"%16.10f %16.10f %16.10f\n", j*latvec[1][1] + latvec[1][1], j*latvec[1][2] + latvec[1][2], j*latvec[1][3] + latvec[1][3] );
fprintf(outputfile,"%16.10f %16.10f %16.10f\n", j*latvec[2][1] + latvec[2][1], j*latvec[2][2] + latvec[2][2], j*latvec[2][3] + latvec[2][3] );
fprintf(outputfile,"%16.10f %16.10f %16.10f\n", j*latvec[3][1] + latvec[3][1], j*latvec[3][2] + latvec[3][2], j*latvec[3][3] + latvec[3][3] );
if (int (b/2.0) == i) cout << " Original lattice vector from a file\n" << endl;
fprintf(outputfile, "\n");
printf("%16.10f %16.10f %16.10f\n", j*latvec[1][1] + latvec[1][1], j*latvec[1][2] + latvec[1][2], j*latvec[1][3] + latvec[1][3] );
printf("%16.10f %16.10f %16.10f\n", j*latvec[2][1] + latvec[2][1], j*latvec[2][2] + latvec[2][2], j*latvec[2][3] + latvec[2][3] );
printf("%16.10f %16.10f %16.10f\n", j*latvec[3][1] + latvec[3][1], j*latvec[3][2] + latvec[3][2], j*latvec[3][3] + latvec[3][3] );
v1[0] = pow(j*latvec[1][1] + latvec[1][1],2) + pow(j*latvec[1][2] + latvec[1][2],2) + pow(j*latvec[1][3] + latvec[1][3],2) ;
v1[1] = pow(j*latvec[2][1] + latvec[2][1],2) + pow(j*latvec[2][2] + latvec[2][2],2) + pow(j*latvec[2][3] + latvec[2][3],2);
v1[2] = pow(j*latvec[3][1] + latvec[3][1],2) + pow(j*latvec[3][2] + latvec[3][2],2) + pow(j*latvec[3][3] + latvec[3][3],2);
for (int k = 0; k < 3; k++) { v1[k]=sqrt(v1[k]);}
printf("%8s %12.4f\n"," volume:", v1[0]*v1[1]*v1[2]*sin (beta*3.14/180) );
printf("\n");
}
break;
fclose(outputfile);
default:
cout << "Invalid option " << endl;
}
return 0;
}