runCharge

#!/bin/bash

    # --------------------------------------------------#
    # PARTIAL CHARGE COMPUTING AND STRUCTURE ANALYSIS   #
    # --------------------------------------------------#   

    # This script prepare everything for RASPA simulations!



red=`tput setaf 1`
green=`tput setaf 2`
reset=`tput sgr0`
adsorbate=charge_equilibration

# --------------------------------------------------#
# CHECK BELOW THE PARAMETERS                        #
# --------------------------------------------------#

cutoff=12; 		# CutOff of the simulation
Cores=17;   		# Cores I would like to use

FreeProcessors=0;
start=$(date +%d%b%y)
mkdir ./frameworks/BoronCIF

echo -e "Here the log-file named COF_analysis.$start.log" >> COF_pore.$start.log

# --------------------------------------------------#
# PARAMETER DECLARATION                             #
# --------------------------------------------------#

echo -e "Name Density H B C O N P S Cl" >> composition.temp
symbol=(H B C O N P S Cl)
mass=(1.00784 10.811 12.0107 15.999 14.0067 30.973762 32.065 35.453)

probe_radius1=1.2 ## (A) for Channel identification and dimensionality
chan_radius=1.2
probe_radius2=1.2 
num_samples=2000

clear

        echo -e "_______________________________________________________________________\n"
        echo " "
        echo "This script computes ${green}Composition${reset}"
        echo "This script computes ${green}Surface area${reset}"
        echo "This script compute ${green}Charge Equilibration${reset}"
        echo " "
        echo -e "\n_______________________________________________________________________\n"



# All the CIF structures in the folder FRAMEWORK are analyzed

for filename in /home/s2216474/RASPA/simulations/share/raspa/structures/cif/TpPa*.cif

do

    FreeProcessors=0 # Assuming there are no Free Processors available, so we can go through the while loop.

    ## Check if a processor is resting and stop until one is ready to go
    while [ $FreeProcessors -le 0 ]
        do

    # --------------------------------------------------#
    # HEADER                                            #
    # --------------------------------------------------#

        clear ## Clean the screen and the header below

            echo -e "_______________________________________________________________________\n"
            echo " "
            echo "This script computes ${green}Stoichiometric Composition${reset}"
            echo "This script computes ${green}Surface area${reset} using Zeo++ (probe radius $probe_radius A)" 
            echo "This script performes ${green}Charge Equilibration${reset} using RASPA"

            echo " "

        ## Check the cores working on RASPA
        Jobs=$(ps ax | grep -c RASPA)
        Jobs=$(($Jobs-1))
        FreeProcessors=$(($Cores-$Jobs))
        echo -e "Cores used ${green}$Jobs / $Cores${reset}.\n"

        ## Print the log to show the progress
        cat COF_analysis.$start.log

        echo -e "\n_______________________________________________________________________\n"

        sleep 0.5s ## Hold on a moment

    done ## Check every 5s if a core is free.

    COFname=$(basename "$filename" .cif)


    ## Check if this is the first time I see this CIF.

#    if [ -d $adsorbate ] #~RDS/ChargedCIF/$COFname ] ## Is there a folder in urea folder?#
#
#    	then ## In the case there is already a folder
#
#      		echo "I already worked on ${red}$COFname${reset}. Let's place it in DONE and pick the next one."
#        #mv $filename ./done
#       		echo -e "$COFname \t$(date)\tSKIPPED" >> COF_analysis.$start.log
#
#    else ## Otherwise#
#
#    	echo -e "\nLet's pick a new one!"

    ## Copy the structure in the main CIF folder of RASPA
    #cp $filename /home/s2216474/RASPA/simulations/share/raspa/structures/cif/$COFname.cif

    TotalMass=0
    N_C=0; N_O=0; N_N=0; N_H=0; 

    n=(0 0 0 0 0 0 0 0)
    massfrac=(0 0 0 0 0 0 0 0)

    TotalMass=0; TotalMol=0
    
    # --------------------------------------------------#
    # COMPOSITION OF CIF (H,B,C,N,S,P)                  #
    # --------------------------------------------------#
    
    for i in {0..7} ## Let's compute atoms presence
    do  
        n[i]=$(grep -o " ${symbol[i]} " "$filename" | wc -l)
        TotalMol=$(echo "${n[i]}+$TotalMol" |  bc -l )
        m[i]=$(echo "${mass[i]}*${n[i]}" |  bc -l )
        TotalMass=$(echo "${m[i]}+$TotalMass" |  bc -l )

    done
        
    echo -ne "\n$COFname\t" >> composition.temp   ## Save results
    echo -ne "$TotalMass\t"  >> composition.temp 
    
    for i in {0..7} ## Let's compute composition
    do  
    
        molarfrac[i]=$(echo "${n[i]}/$TotalMol" |  bc -l )
        massfrac[i]=$(echo "${m[i]}/$TotalMass" |  bc -l )

        echo -ne "${molarfrac[i]}\t"  >> composition.temp   ## Save results in a file
        echo -ne "${massfrac[i]}\t" >> composition.temp     ## Save results in a file
    done
   
    echo -e "Composition analysis: Done."
       
            ##echo -e "Boron concentration ${molarfrac[1]}"
            ##echo "$(echo "${molarfrac[1]} < 0.00001" | bc -l)"
    
    ## Let's check if there are B atoms in the CIF structure and skip them.
    if  [ $(echo "${molarfrac[1]} < 1" | bc -l) -eq 1 ] 
    
    then    
    cd ./$adsorbate
    mkdir -p $COFname
    echo "Building a folder for ${red}$COFname${reset} and copying required files."

    cp ../start/* ./$COFname
    cd ./$COFname

    rm ./simulation.input >> outputfile


    # --------------------------------------------------#
    # TOPOLOGICAL ANALYSIS OF CIF                       #
    # --------------------------------------------------#
    
    
    #echo -e "Done. Pore diameters."
    ## echo -e "Done. \n Channel identification and dimensionality."
    #/home/s2216474/zeo++-0.3/network -ha -sa "$probe_radius" "$probe_radius" 5000 ../../$filename >> outputfile
    ##echo -e "Done. \n Channel identification and dimensionality."    
    ##../../../../../zeo++-0.3/network -ha -chan 1.2 ../../$filename >> channel.txt 
    ##echo -e "Done. \n Vornoi."
    ##../../../../../zeo++-0.3/network -r -nt2 ../../$filename
    ##echo -e "Done. \n Spheres."
    ##../../../../../zeo++-0.3/network -gridG ../../$filename
    ##echo -e "Done. \n Spheres."
    ##../../../../../zeo++-0.3/network -gridBOV ../../$filename
    ##../../../../../zeo++-0.3/network -ray_atom 1.2 1.2 500 outputfile.ray ../../$filename 
    ##../../../../../zeo++-0.3/network  -axs 1.6 outputfile.axs ../../$filename 
    ##echo -e "Done. \n Surface area."    
    ##../../../../../zeo++-0.3/network -ha -psd 1.2 1.2 50000 ../../$filename >> outputfile
    ##echo -e "Done. \n Structure analysis."
    ##../../../../../zeo++-0.3/network -strinfo ../../$filename >> outputfile
    
    
    # --------------------------------------------------#
    # PREPARE THE INPUT FILE FOR CHARGE EQUILIBRATION   #
    # --------------------------------------------------#    
    
    echo "Writing simulation input file!"
    
    echo    "SimulationType MonteCarlo
NumberOfCycles 0
InitializationCycles 0
Forcefield Local
Framework 0
FrameworkName $COFname
UnitCells 1 1 1 ## To be understood if this is enough!
ChargeFromChargeEquilibration yes
ChargeEquilibrationPeriodic yes" >> ./simulation.input

./run > outputfile 2>&1 &  ## Run the Charge Equilibration in background

cd ../../
echo -e "Launched Charge Equilibration on $COFname . Done!"
echo -e "$COFname \t$(date)\tRUN" >> COF_analysis.$start.log  ## Report the CIF in the log

## Wanna see the input?
## more ./simulation.input   

else ## This is the case of a Boron containing CIF structure 
    echo -e "${red} $COFname contains Boron!${reset} Let's skip this structure."
    echo -e "$COFname \t$(date)\tBORON " >> COF_analysis.$start.log
    ## Sort these CIF files, place them in a folder and forget about them for the moment
    mv $filename ./BoronCIF
fi
#fi

echo -e "\n_______________________________________________________________________\n"

sleep 2s ## Just a little break! 

done ## Let's start with a new one!


mv *.log ./log/ ## Place the log in a safe place!

echo -e "\n The charge equilibration is over! Let's move forward with the Widom. \n"
##./runHenry ## Recall the script for this purpose.