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Kick-Fukui_Algorithm.pl
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Kick-Fukui_Algorithm.pl
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#!/usr/bin/env perl
#
# Write code:
# Diego Inostrosa & Osvaldo Yañez Osses
# contact: [email protected]
# Modules
use strict;
use Benchmark; #entrega cuando demora el proceso, cuanto de CPU utilizó, etc
use Cwd qw(abs_path);
use File::Basename;
use List::Util qw(min max);
use Scalar::Util qw(looks_like_number);
# install: sudo cpan Parallel::ForkManager
use Parallel::ForkManager;
# install: sudo cpan Math::Matrix
use Math::Matrix;
#
#
# Number of process
my $ncpus = 100;
# Weight spherical restriction algorithm
#
my $weight_spherical = 10.0;
#my $weight_spherical = 2.0;
#
#
###########################
# Configure file variables
my $num_atoms_global;
my $num_basin_global;
my $Num_of_geometries;
my $XYZSize;
my $Box_x;
my $Box_y;
my $Box_z;
my $decision;
my $sort_option;
my $duplicate_mol;
my $output_file;
my $Final_File;
#
my @ValueJ = ();
#
my $Tam1 = 0;
my $Tam2 = 0;
#
my %HashCoordsAttra = ();
my %HashDist = ();
my %HashMult = ();
# Default is 1 unless factor is given.
my $Box_Multiplication_Factor = 1;
my $BoxAutomatic = 1;
#
my %Atomic_radii = ( 'H' => '1.00', 'Li' => '1.45', 'Be' => '1.05', 'B' => '0.85',
'C' => '0.70', 'N' => '0.65', 'O' => '1.35', 'F' => '0.50',
'Na' => '1.80', 'Mg' => '1.50', 'Al' => '1.25', 'Si' => '1.10',
'P' => '1.00', 'S' => '1.00', 'Cl' => '1.00', 'K' => '2.20',
'Ca' => '1.80', 'Sc' => '1.60', 'Ti' => '1.40', 'V' => '1.35',
'Cr' => '1.40', 'Mn' => '1.40', 'Fe' => '1.40', 'Co' => '1.35',
'Ni' => '1.35', 'Cu' => '1.35', 'Zn' => '1.35', 'Ga' => '1.30',
'Ge' => '1.25', 'As' => '1.15', 'Se' => '1.15', 'Br' => '1.15',
'Rb' => '2.35', 'Sr' => '2.00', 'Y' => '1.80', 'Zr' => '1.55',
'Nb' => '1.45', 'Mo' => '1.45', 'Tc' => '1.35', 'Ru' => '1.30',
'Rh' => '1.35', 'Pd' => '1.40', 'Ag' => '1.60', 'Cd' => '1.55',
'In' => '1.55', 'Sn' => '1.45', 'Sb' => '1.45', 'Te' => '1.40',
'I' => '1.40', 'Cs' => '2.60', 'Ba' => '2.15', 'La' => '1.95',
'Ce' => '1.85', 'Pr' => '1.85', 'Nd' => '1.85', 'Pm' => '1.85',
'Sm' => '1.85', 'Eu' => '1.85', 'Gd' => '1.80', 'Tb' => '1.75',
'Dy' => '1.75', 'Ho' => '1.75', 'Er' => '1.75', 'Tu' => '1.75',
'Yb' => '1.75', 'Lu' => '1.75', 'Hf' => '1.55', 'Ta' => '1.45',
'W' => '1.35', 'Re' => '1.35', 'Os' => '1.30', 'Ir' => '1.35',
'Pt' => '1.35', 'Au' => '1.35', 'Hg' => '1.50', 'Tl' => '1.90',
'Bi' => '1.60', 'Po' => '1.90', 'Ra' => '2.15', 'Ac' => '1.95',
'Th' => '1.80', 'Pa' => '1.80', 'U' => '1.75', 'Np' => '1.75',
'Pu' => '1.75', 'Am' => '1.75', default=> '0.8' );
###################################
# Regular expression
sub ltrim { my $s = shift; $s =~ s/^\s+//; return $s };
sub rtrim { my $s = shift; $s =~ s/\s+$//; return $s };
sub trim { my $s = shift; $s =~ s/^\s+|\s+$//g; return $s };
###################################
# Read .frag file
sub FragFileReader{
my ($taffFile) = @_;
#open tf file
my @information = ();
if(open(FRAG,$taffFile)){
print "MESSAGE Reading File $taffFile\n";
@information=<FRAG>;
}else{
print "ERROR Can't open $taffFile\n";
exit(1);
}
close(FRAG);
# Variable creations
my $aux_na = 0;
my $aux_ba = 0;
my @array_integral = ();
my @array_X = ();
my @array_Y = ();
my @array_Z = ();
my @array_atoms = ();
my @array_atoms_x = ();
my @array_atoms_y = ();
my @array_atoms_z = ();
#set data in varbiales
foreach my $line (@information){
chomp($line);
my @data=split(" ",$line);
if($data[0] eq "X"){
#if($data[4])
push @array_integral, $data[4];
push @array_X, $data[1];
push @array_Y, $data[2];
push @array_Z, $data[3];
$aux_ba++;
}else{
push @array_atoms, $data[0];
push @array_atoms_x, $data[1];
push @array_atoms_y, $data[2];
push @array_atoms_z, $data[3];
$aux_na++;
}
}
my $MaxIntegral = max(@array_integral);
my $CutUmbral = $MaxIntegral/1000.0;
#
# Counter of atoms and basins
my @array_set_atoms = ([@array_atoms],
[@array_atoms_x],
[@array_atoms_y],
[@array_atoms_z]);
my @array_set_basin = (0,
[@array_integral],
0,
[@array_X],
[@array_Y],
[@array_Z],
0,
0);
#
# This code block and eliminate negative and low integals values
# dump (@array_set_basin);
for (my $i = 0; $i < $aux_ba; $i++) {
#print "Viendo $array_set_basin[1][$i] en $i\n";
if($array_set_basin[1][$i] < $CutUmbral){
# print "Eliminando.. $array_set_basin[1][$i]\n";
splice @{$array_set_basin[1]}, $i, 1;
splice @{$array_set_basin[3]}, $i, 1;
splice @{$array_set_basin[4]}, $i, 1;
splice @{$array_set_basin[5]}, $i, 1;
$aux_ba--;
$i--;
}
}
# print "AFTER\n";
# dump (@array_set_basin);
$num_atoms_global=$aux_na;
$num_basin_global=$aux_ba;
#
my @matrix = ([@array_set_atoms],
[@array_set_basin]);
return @matrix;
}
###################################
# Box size manipulation
sub BoxCoordinates{
my ($f1,$f2) = @_;
#
my @frag1 = @{$f1};
my @frag2 = @{$f2};
#llama al otro metodo y luego suma los tamaños
my $dist1 = BoxSizeCalculation(@frag1);
my $dist2 = BoxSizeCalculation(@frag2);
#
$Tam1 = $dist1;
$Tam2 = $dist2;
#
my $sum = $dist2+$dist1;
# Box size = (frag1+frag2) * 0.8 (Default).
my $Box = $sum * $Box_Multiplication_Factor;
# This means, maximum size of each fragments, the we choose only X of the space
$Box_x = $Box;
$Box_y = $Box;
$Box_z = $Box;
}
###################################
# Get optimal size
sub BoxSizeCalculation{
my @frag = @_;
my @x = ();
my @y = ();
my @z = ();
my @at = ();
foreach my $line(@frag){
($at[++$#at],$x[++$#x],$y[++$#y],$z[++$#z]) = split(' ',$line);
}
my @dist = ();
push(@dist, MinMax(@x));
push(@dist, MinMax(@y));
push(@dist, MinMax(@z));
my @sorted = sort { $b <=> $a } @dist;
return $sorted[0];
}
###################################
# Get maximun or minimun from an array, Box use
sub MinMax{
# We got the biggest distance (X Y Z)
my @array = @_;
my($min, $max);
for(@array){
$min = $_ if !$min || $_ < $min;
$max = $_ if !$max || $_ > $max
};
my $dist = $max-$min;
return $dist;
}
###################################
# Read files
sub clear_data{
my (@data)=@_;
my @datos=();
foreach my $info(@data){
my @tmp=split(' ', $info);
$datos[++$#datos]=[@tmp];
}
# Print $datos[0][0]
# First [] indicates the position, or line in the .frag file.
# Second [] indicates data in specific:
# 0 = Atom type.
# 1 = X
# 2 = Y
# 3 = Z
return @datos;
}
###################################
# Verification
sub verification{
my ($a1, $a2, $dist)=@_;
# hash values
my $v1 = $Atomic_radii{$a1} || $Atomic_radii{default};
my $v2 = $Atomic_radii{$a2} || $Atomic_radii{default};
my $sum = $v1+$v2;
my $resultado;
# Steric effects if radii_1 + radii_2 < distance
if($dist <= $sum){
# Steric problem
$resultado = 1;
}else{
$resultado = 0;
}
return $resultado;
}
###################################
# Steric Impediment
sub steric_impediment{
# array are send by reference
my ($cords1,$cords2)=@_;
# arrays
my @coords1=@{$cords1};
my @coords2=@{$cords2};
# get size
my $distance;
my ($final_trial, $resultado)=(0, 0);
# all the atoms from the first structure
for (my $i=0; $i<scalar(@coords1);$i++){
# second structure
for(my $j=0; $j<scalar(@coords2);$j++){
# only atoms, not basins
$distance=distance_point($coords1[$i][1],$coords1[$i][2],$coords1[$i][3],$coords2[$j][1],$coords2[$j][2],$coords2[$j][3]);
$final_trial=$final_trial+verification($coords1[$i][0],$coords2[$j][0],$distance);
if($final_trial==1){
$resultado=1;
last;
}
}
}
return $resultado;
}
###################################
# Distance between one point to all other in a coord xyz
sub medium_point {
# array coords basin 1 and basin 2
my ($coords_1,$coords_2) = @_;
my @arr1 = @{$coords_1};
my @arr2 = @{$coords_2};
#
my $med_x = ( ($arr1[0] + $arr2[0]) / 2 );
my $med_y = ( ($arr1[1] + $arr2[1]) / 2 );
my $med_z = ( ($arr1[2] + $arr2[2]) / 2 );
#
my @medium = ($med_x, $med_y, $med_z);
return @medium;
}
###################################
# Distance between one point to all other in a coord xyz
sub distance_point {
# array coords basin 1 and basin 2
my ($p1,$p2,$p3, $x1, $y1, $z1) = @_;
# measure distance between two point
my $dist = sqrt(
($x1-$p1)**2 +
($y1-$p2)**2 +
($z1-$p3)**2
);
return $dist;
}
###################################
# Parsing name atom
sub parsing_name_atom {
my ($atom_set) = @_;
my @array = ();
@array = split('_', $atom_set);
# return array
return $array[0];
}
###################################
# This function opens a file, and returns the info in an array of lines
sub read_file {
# filename
my ($input_file) = @_;
my @lines = ();
my @array = ();
# open file
open(FILE, "<", $input_file ) || die "Can't open $input_file: $!";
@lines = <FILE>;
close (FILE);
# loop
foreach my $a (@lines){
chomp ($a);
$array[++$#array] = $a;
}
# return array
return @array;
}
###################################
# compute the center of mass
sub measure_center {
my ($coord_x,$coord_y,$coord_z) = @_;
my $num_data = scalar (@{$coord_x});
my @array = ();
my $weight = 1;
# variable sum
my $sum_weight = 0;
my $sum_x = 0;
my $sum_y = 0;
my $sum_z = 0;
for ( my $j = 0 ; $j < $num_data ; $j = $j + 1 ){
$sum_weight+= $weight;
$sum_x+= $weight * @$coord_x[$j];
$sum_y+= $weight * @$coord_y[$j];
$sum_z+= $weight * @$coord_z[$j];
}
my $com_x = $sum_x / $sum_weight;
my $com_y = $sum_y / $sum_weight;
my $com_z = $sum_z / $sum_weight;
# array
@array = ($com_x,$com_y,$com_z);
# return array
return @array;
}
###################################
# Returns the additive inverse of v(-v)
sub vecinvert {
my ($center_mass) = @_;
my @array = ();
foreach my $i (@$center_mass) {
my $invert = $i * -1;
$array[++$#array] = $invert;
}
# return array
return @array;
}
###################################
# Returns the vector sum of all the terms
sub vecadd {
my ($coord_x,$coord_y,$coord_z,$vecinvert_cm ) = @_;
my $num_data = scalar (@{$coord_x});
my @array = ();
my $sum_coord_x;
my $sum_coord_y;
my $sum_coord_z;
# array
my @array_x = ();
my @array_y = ();
my @array_z = ();
for ( my $i = 0 ; $i < $num_data ; $i = $i + 1 ){
$sum_coord_x = @$coord_x[$i]+@$vecinvert_cm[0] ;
$sum_coord_y = @$coord_y[$i]+@$vecinvert_cm[1] ;
$sum_coord_z = @$coord_z[$i]+@$vecinvert_cm[2] ;
# save array
$array_x[++$#array_x] = $sum_coord_x;
$array_y[++$#array_y] = $sum_coord_y;
$array_z[++$#array_z] = $sum_coord_z;
}
@array = ( [@array_x],
[@array_y],
[@array_z] );
# return array
return @array;
}
###################################
# Focus on the origin of molecular systems
sub CenterMolecule {
my ($input, $energy, $total_num)=@_;
my @problematic_molecule=@{$input};
my @coord_x=@{$problematic_molecule[1]};
my @total_array = ();
#
my @array_center_mass = measure_center(\@{$problematic_molecule[1]},\@{$problematic_molecule[2]},\@{$problematic_molecule[3]});
my @array_vecinvert = vecinvert(\@array_center_mass);
my @array_catersian = vecadd (\@{$problematic_molecule[1]},\@{$problematic_molecule[2]},\@{$problematic_molecule[3]},\@array_vecinvert);
#
my @at = @{$problematic_molecule[0]};
my @cx = @{$array_catersian[0]};
my @cy = @{$array_catersian[1]};
my @cz = @{$array_catersian[2]};
#
open(FILE, ">>Mol_Center.xyz");
print FILE "$total_num\n";
print FILE "$energy\n";
for (my $i=0; $i < scalar(@at) ; $i++) {
my $x_coord = sprintf '%.6f', $cx[$i];
my $y_coord = sprintf '%.6f', $cy[$i];
my $z_coord = sprintf '%.6f', $cz[$i];
print FILE "$at[$i]\t$x_coord\t$y_coord\t$z_coord\n";
}
close (FILE);
}
###################################
# Generation of random co-ordinates
sub gen_xyz {
my $x = rand($Box_x);
my $y = rand($Box_y);
my $z = rand($Box_z);
my $x_coord = sprintf '%.6f', $x;
my $y_coord = sprintf '%.6f', $y;
my $z_coord = sprintf '%.6f', $z;
my @coords =($x_coord, $y_coord, $z_coord);
return @coords;
}
###################################
# phi, theta, psi
sub gen_ptp {
my $pi = 3.14159265;
my $phi = sprintf '%.6f', rand()*2*$pi;
my $theta = sprintf '%.6f', rand()*2*$pi;
my $psi = sprintf '%.6f', rand()*2*$pi;
my @angles =($phi, $theta, $psi);
return @angles;
}
###################################
# Generating .cart files
sub cart_file_write {
my ($name_without_extension,$num_atom, $num_basin, @matrix)=@_;
open(FILE, ">$name_without_extension.cart");
for(my $i=0; $i<$num_atom;$i++){
print FILE "$matrix[0][0][$i]\t$matrix[0][1][$i]\t$matrix[0][2][$i]\t$matrix[0][3][$i]\n";
}
for(my $j=0; $j<$num_basin;$j++){
print FILE "X\t$matrix[1][3][$j]\t$matrix[1][4][$j]\t$matrix[1][5][$j]\n"
}
close (FILE);
}
###################################
# multiplication of attractors
sub basin_integral_multi{
my ($m1, $m2,$basin1,$basin2)=@_;
my @matrix1=@{$m1};
my @matrix2=@{$m2};
my @array_multi=();
for(my $i=0; $i<$basin1; $i++){
for(my $j=0; $j<$basin2; $j++){
my $tmp=$matrix1[1][1][$i]*$matrix2[1][1][$j];
push(@array_multi,$tmp);
}
}
return @array_multi;
}
###################################
# Cartesian distance measuring
sub distance_medition{
my ($ba1, $ba2)=@_;
my @big_array1=@{$ba1};
my @big_array2=@{$ba2};
my @dist_total=();
#
my $count = 0;
#
for (my $i = 0; $i < scalar (@{$big_array1[2]}); $i++) {
for (my $j = 0; $j < scalar (@{$big_array2[2]}); $j++) {
my $tmp_dist = distance_point ( $big_array1[1][$i],$big_array1[2][$i],$big_array1[3][$i], $big_array2[1][$j],$big_array2[2][$j],$big_array2[3][$j]);
push (@dist_total,$tmp_dist);
#
my $key = $count;
$HashCoordsAttra{$key} ="$big_array1[1][$i],$big_array1[2][$i],$big_array1[3][$i] = $big_array2[1][$j],$big_array2[2][$j],$big_array2[3][$j]" ;
$HashDist{$key} = $tmp_dist;
$count++;
}
}
return @dist_total;
}
###################################
# Here, magics happends
# Essencially the fragments coordinates are randomly rotated and traslatated
sub position_change_fragment{
my(@FragLines) = @_;
# Rotate
my @base_angles = gen_ptp();
my $phi = $base_angles[0];
my $theta = $base_angles[1];
my $psi = $base_angles[2];
# Translate
my @base_xyz = gen_xyz();
my $base_x = $base_xyz[0];
my $base_y = $base_xyz[1];
my $base_z = $base_xyz[2];
# Do the trig
my $cos_phi = sprintf '%.6f', cos($phi);
my $cos_theta = sprintf '%.6f', cos($theta);
my $cos_psi = sprintf '%.6f', cos($psi);
my $sin_phi = sprintf '%.6f', sin($phi);
my $sin_theta = sprintf '%.6f', sin($theta);
my $sin_psi = sprintf '%.6f', sin($psi);
# Make the rotation matrix
my $D = new Math::Matrix ([$cos_phi,$sin_phi,0],[-$sin_phi,$cos_phi,0],[0,0,1]);
my $C = new Math::Matrix ([1,0,0],[0,$cos_theta,$sin_theta],[0,-$sin_theta,$cos_theta]);
my $B = new Math::Matrix ([$cos_psi,$sin_psi,0],[-$sin_psi,$cos_psi,0],[0,0,1]);
my $A = $B->multiply($C)->multiply($D);
#
my @ar_x = ();
my @ar_y = ();
my @ar_z = ();
my @coords = ();
#
while (my $Fline = shift (@FragLines)) {
my @Cartesians = split '\s+', $Fline;
my ($Atom_label, @orig_xyz) = @Cartesians;
my $matrix_xyz = new Math::Matrix ([$orig_xyz[0],$orig_xyz[1],$orig_xyz[2]]);
my $trans_xyz = ($matrix_xyz->transpose);
my $rotated_xyz = $A->multiply($trans_xyz);
my @new_xyz = split '\n+',$rotated_xyz;
# Save rotated fragment
push(@new_xyz,$Atom_label);
#
my $new_x = $base_x + $new_xyz[0];
my $new_y = $base_y + $new_xyz[1];
my $new_z = $base_z + $new_xyz[2];
if($new_xyz[3] eq "X"){
push (@ar_x,$new_x);
push (@ar_y,$new_y);
push (@ar_z,$new_z);
}else{
push (@coords,"$Atom_label\t$new_x\t$new_y\t$new_z");
}
}
#
my @bigarray = ([@coords],[@ar_x],[@ar_y],[@ar_z]);
return @bigarray;
}
###################################
# Equation
sub equation{
my ($multi, $dist) = @_;
my @b_multi = @{$multi};
my @b_dist = @{$dist};
my $sum=0;
for (my $i = 0; $i < scalar (@b_multi); $i++) {
#print "f+ * f- = $b_multi[$i] with distance of $b_dist[$i]\t\n";
my $division = ( $b_multi[$i] / $b_dist[$i] );
#print "f+ * f- = $b_multi[$i] with distance of $b_dist[$i]\t Division: $division\n";
$sum+=$division;
}
return $sum;
}
###################################
# write xyz file
sub write_xyz_file_center{
my ($pid,$arr_center, $atom) = @_;
my @arr = @{$arr_center};
open (XYZ,">>tmp$pid.tmp");
print XYZ "$atom\t$arr[0]\t$arr[1]\t$arr[2]\n";
close (XYZ);
}
###################################
# write xyz file data
sub write_xyz_file_header{
#write only the header for each tmp file
my ($pid, $atoms_total, $sum)=@_;
open(XYZ,">>tmp$pid.tmp");
print XYZ "$atoms_total\n";
print XYZ "E = $sum\n";
close (XYZ);
}
###################################
# write xyz file
sub write_xyz_file{
#write the coordinate information for each tmp file
my ($pid, $Attract, @big_array )=@_;
#
my @tmpr = @{$Attract};
#
open(XYZ,">>tmp$pid.tmp");
my @coords =clear_data(@{$big_array[0]});
for(my $i=0; $i<scalar(@coords); $i++){
#
#my $c_x = sprintf '%.6f', $coords[$i][1];
#my $c_y = sprintf '%.6f', $coords[$i][2];
#my $c_z = sprintf '%.6f', $coords[$i][3];
#
print XYZ "$coords[$i][0]\t$coords[$i][1]\t$coords[$i][2]\t$coords[$i][3]\n";
}
close (XYZ);
}
###################################
# sort in descending order energies
sub sort_energies{
# Simple sort, uses hash for sorting
my @files = glob "*.tmp";
my ($na, $me) = @_;
my @energies = ();
my @sorted_numbers;
my %super;
my $natom;
foreach my $file (@files){
# Open files .tmp
open (TMP, "<$file") || die "cannot open $file in sort subroutine\n";
my @lines=<TMP>;
close(TMP);
#
$natom = $lines[0];
my $energy = $lines[1];
$energy=~s/(E = )?//g;
chomp($energy);
push(@energies, $energy);
my $coords="";
#
foreach $a (2..($#lines)){
$coords=$coords.$lines[$a];
}
$super{$energies[$#energies]}=$coords;
unlink "$file";
}
# Potencial
@sorted_numbers = sort { $a <=> $b } @energies;
# Fukui
# @sorted_numbers = sort { $b <=> $a } @energies;
@ValueJ = @sorted_numbers;
# write inputfile .XYZ
open(NEW, ">tmp_kick-fukui.xyz");
my $aux = 0;
#
foreach my $item (@sorted_numbers){
if($aux < $XYZSize){
print NEW "$natom", "E = $item\n",$super{$item};
}else{
last;
}
$aux++;
}
close(NEW);
}
#####################################
# Normal order
sub unify_tmp_files_noSort{
my ($na, $me)=@_;
my @files =glob "*.tmp";
open(NEW, ">tmp_kick-fukui.xyz");
#
my @energies = ();
#
foreach my $file (@files){
# Open files .tmp
open (TMP, "<$file") || die "cannot open $file in sort subroutine\n";
my @lines=<TMP>;
close(TMP);
#
my $energy = $lines[1];
$energy=~s/(E = )?//g;
chomp($energy);
push(@energies, $energy);
}
#
@ValueJ = sort { $b <=> $a } @energies;
#
my $aux = 0;
foreach my $file (@files){
open (TMP, "<$file") || die "cannot open $file in sort subroutine\n";
my @lines=<TMP>;
close(TMP);
#
if($aux < $XYZSize){
print NEW @lines;
}else{
last;
}
$aux++;
}
close(NEW);
#
foreach my $file (@files){
unlink "$file";
}
}
#####################################
# Logo Kick-Fukui
sub logo {
print "\n";
print " ____ __.__ __ ___________ __ .__ \n";
print " | |/ _|__| ____ | | __ \\_ _____/_ __| | ____ __|__| \n";
print " | < | |/ ___\\| |/ / ______ | __)| | \\ |/ / | \\ | \n";
print " | | \\| \\ \\___| < /_____/ | \\ | | / <| | / | \n";
print " |____|__ \\__|\\___ >__|_ \\ \\___ / |____/|__|_ \\____/|__| \n";
print " \\/ \\/ \\/ \\/ \\/ \n";
print "\n\n";
print " Search global minimum structures of atomic clusters and molecules in the gas phase,\n";
print " using as a Coulomb interaction between Fukui functions-based method \n";
print "\n";
}
###################################
# Configuration input file
sub ConfigFileReader{
#
my $configfile = $ARGV[0];
#
if (not defined $configfile) {
die "\n Kick-Fukui_Algorithm must be run with:\n\n Usage :\n\tperl $0 [configure-file]\n
\n Help :\n\tperl $0 -help \n\n\n";
exit(1);
}
#
if($configfile=~/-help/i) {
show_help();
exit (1);
}
# Open configure file
open(CONFIG,$configfile) or die "ERROR Configuration file doesn't exist\n\n";
my @lines=<CONFIG>;
close(CONFIG);
#
my $aux = 0;
my ($frag1, $frag2);
foreach my $line(@lines){
chomp($line);
my $letter = substr($line, 0, 1);
my ($key, $value)=split("=",$line);
# Check repository
# the char # marks a commentary
if($letter ne "#" && $line ne ""){
$value = trim($value);
#
if($key=~/initial_species/i){
$Num_of_geometries=$value;
$aux++;
}
#
if ($key=~/final_species/i) {
$XYZSize=$value;
$aux++;
}
#
if($key=~/mol_1/i){
$frag1 = $value;
$aux++;
}
#
if($key=~/mol_2/i){
$frag2 = $value;
$aux++;
}
#
if($key=~/box_size_factor/i){
my @box=split(",",$value);
if(scalar(@box)==1){
$Box_Multiplication_Factor=$value;
}elsif(scalar(@box)==3){
if(looks_like_number($box[0]) && looks_like_number($box[1]) && looks_like_number($box[2])){
print "MESSAGE Box Size given by user\n";
$BoxAutomatic=2;
$Box_x = $box[0];
$Box_y = $box[1];
$Box_z = $box[2];
}else{
print "ERROR Box coordinates are not numeric\n";
exit(1);
}
}else{
print "ERROR Box Size error, usage box_size_factor = X,Y,Z \n";
exit(1);
}
}
#
if($key=~/energy_order/i){
$sort_option = $value;
if (($sort_option=~/yes/i )) {
print "MESSAGE Choose Sort by Descending Order \n";
} elsif (($sort_option=~/no/i )) {
print "MESSAGE Select Stochastic Order \n";
} else {
print "ERROR Set the Correct Option energy_order = YES/NO \n";
exit (1);
}
}
#
if($key=~/duplicate_species/i){
$duplicate_mol = $value;
if (($duplicate_mol=~/yes/i )) {
print "MESSAGE Grigoryan-Springborg's Algorithm \n";
} elsif (($duplicate_mol=~/no/i )) {
print "MESSAGE Don't Select Duplicates \n";
} else {
print "ERROR Set The Correct Option duplicate_species YES/NO \n";
exit (1);
}
}
#
if($key=~/output_file_name/i){
$output_file=$value;
$aux++;
}
}
}
if($aux!=5){
print "ERROR Wrong number of params in $ARGV[0]\naux = $aux\n";
exit(1);
}
return ($frag1, $frag2);
}
####################################
# Summary Kick-Fukui Algorithm
sub resume_log_file {
my ($na,$me,$timeS,$timeE,$timeT)=@_;
#
print "\n";
print " <> Summary Kick-Fukui Algorithm <> \n\n";
# Sample Size
print " * Sample Size: $Num_of_geometries\n";
# Molecules f+ and f-
print " * Molecules \n";
print " f+ : $na.frag \n";
print " f- : $me.frag \n";
# Box size
my $c_x = sprintf '%.2f', $Box_x;
my $c_y = sprintf '%.2f', $Box_y;
my $c_z = sprintf '%.2f', $Box_z;
print " * Box size : $c_x Å x $c_y Å x $c_z Å\n";
# Output file xyz
print " * Output File: $Final_File\n";
#
my $J_value = sprintf '%.6f', $ValueJ[0];
print " * Maximun Coulombic-Interaction Value (J) : $J_value\n";
#
print "\n <> Performance Data <> \n\n";
# Total number of process
print " * N° Process : $ncpus\n";
# Start of the program
print " * Start : $timeS\n";
# Final execution of the programme
print " * End : $timeE\n";
# Execution time
print " * Execution time :$timeT\n\n";
#
print "MESSAGE Normal Termination Kick-Fukui Algorithm\n\n\n";
#
}
###################################
# Help
sub show_help {
print " <> To use Kick-Fukui Algorithm <> \n\n";
#
print "\n";
print " * The Initial Population size (1000N, N = Atoms number) \n";
print "\t initial_species = 1000 \n";
print "\n";
print " * Number of final geometries \n";
print "\t final_species = 100 \n";
print "\n";
print " * * Name of molecular species in the simulation \n";
print " * File with the nucleophilic Fukui function \n";
print "\t Mol_1 = f+FileCoords.frag \n";
print " * File with the electrophilic Fukui function \n";
print "\t Mol_2 = f-FileCoords.frag \n";
print "\n";
print " * Box size the sum of the sides from both molecules multiply for a factor (Default 1) \n";
print " * The factor size or size of the box (in Angstroms) length, width, and height \n";
print "\t box_size_factor = 0.8 or box_size_factor = 10, 10, 10\n";
print "\n";
print " * Order Coulombic-Interaction Value (J) in a descending (YES) or scholastic (NO) manner \n";
print "\t energy_order = YES \n";
print "\n";
print " * Search for duplicate molecular species (YES/NO) \n";
print "\t duplicate_species = NO \n";
print "\n";
print " * Output xyz file name (Default name Kick-Fukui-Output.xyz) \n";
print "\t output_file_name = NameOutputFile.xyz \n";
print "\n";
}
###################################
# MAIN
my @matrix_1;
my $atoms_num_1;
my $basin_num_1;
# extension 1
my $without_extension_1;
#
my @matrix_2;
my $atoms_num_2;
my $basin_num_2;
# extension 2
my $without_extension_2;
#
logo ();
my $tiempo_inicial = new Benchmark; #funcion para el tiempo de ejecucion del programa
my $datestringStart = localtime();
# delete .tmp files
unlink glob "*.tmp";
unlink ("$output_file.xyz");
#
# Read configure file
my ($file_name_1, $file_name_2) = ConfigFileReader();
#
# Read .frag files
#
@matrix_1 = FragFileReader($file_name_1);
$atoms_num_1 = $num_atoms_global;
$basin_num_1 = $num_basin_global;
# extension
$file_name_1=(split("/",$file_name_1))[-1];
( $without_extension_1 = $file_name_1) =~ s/\.[^.]+$//;
#
@matrix_2 = FragFileReader($file_name_2);
$atoms_num_2 = $num_atoms_global;
$basin_num_2 = $num_basin_global;
# extension
$file_name_2=(split("/",$file_name_2))[-1];
($without_extension_2 = $file_name_2) =~ s/\.[^.]+$//;
#
#
# Creation of .cart files
cart_file_write($without_extension_1,$atoms_num_1,$basin_num_1,@matrix_1);
cart_file_write($without_extension_2,$atoms_num_2,$basin_num_2,@matrix_2);
# Reading .cart file
open(FRAG1,"$without_extension_1.cart" ) or die "ERROR Unable to open fragment file: $without_extension_1.cart";
open(FRAG2,"$without_extension_2.cart" ) or die "ERROR Unable to open fragment file: $without_extension_2.cart";
my @f1=<FRAG1>;
my @f2=<FRAG2>;
close(FRAG1);
close(FRAG2);
unlink glob "*.cart";
#
# Parallel processing
my $pm = new Parallel::ForkManager($ncpus);
if ($BoxAutomatic == 1){
BoxCoordinates(\@f1,\@f2);
}
#
# The integral value for each attractor doesn't change moving the fragments.
# So the multiplication between atractor (integral) is only done once.
my @multi = basin_integral_multi(\@matrix_1, \@matrix_2, $basin_num_1, $basin_num_2);
#
foreach my $iteration(1 .. $Num_of_geometries){
$pm->start($iteration) and next;
# All children process have their own random
srand();
# To verify steric impediment
my $decision = 1;
#
my @resume1;
my @resume2;
#
while($decision!=0){
# Randomize atoms and basin positions
@resume1 = position_change_fragment(@f1);
@resume2 = position_change_fragment(@f2);
# Get atoms coordinates
my @coords_1 = clear_data(@{$resume1[0]});
my @coords_2 = clear_data(@{$resume2[0]});
# Verify for steric impediment, 1 yes, 0 no;
$decision = steric_impediment(\@coords_1, \@coords_2);
}
###################################
# Spherical restriction algorithm
#
# Attractors X=@{$resume1[1]}, Y=@{$resume1[2]},Z=@{$resume1[3]}
# measure center of mass
my @array_center_mass_attrac1 = measure_center(\@{$resume1[1]},\@{$resume1[2]},\@{$resume1[3]});
my @array_center_mass_attrac2 = measure_center(\@{$resume2[1]},\@{$resume2[2]},\@{$resume2[3]});