FreqQRCScript to run the program
#!/bin/csh
if (-e $1) then
java FreqQRC $*
else
echo This class reads in a jaguar frequency calculation file: $1.out
echo and produces a new cartesian file: $1.fdt
echo with coordinates with the
echo first vibrational frequency added, and separately, subtracted.
echo These files can then be minimised as pseudo IRC calculation.
echo
echo The first step is to find cartesian coordinates describing the final
echo geometry. These are usually marked 'final geometry' unless the
echo calculation was not a minimisation, in which case they are
echo 'Input geometry'
echo
echo Once these have been read, go on to find frequencies.
echo This program will just read the first - the negative one
echo if there is a negative one.
echo
echo A second parameter will be used to modify the degree of distortion
echo The default value is 1.0
echo
echo The first line of the .ftd file should end with the energy, in
echo hartrees. Some GAMESS files do not include this, and it should
echo be added by hand if the .ftd file is going to be used in a
echo FindQRC calculation.
echo
endif
Java code
import java.io.*;
class FreqQRC {
/**
* This class reads in a jaguar frequency calculation file
* or a GAMESS frequency calculation file
* and produces a new cartesian file with coordinates with the
* first vibrational frequency added, and separately, subtracted.
* These files can then be minimised as pseudo IRC calculation.
*
* The first step is to find cartesian coordinates describing the final
* geometry. These are usually marked 'final geometry' unless the
* calculation was not a minimisation, in which case they are
* 'Input geometry'
*
* Once these have been read, go on to find frequencies.
* This program will just read the first - the negative one
* if there is a negative one.
*/
public static void main(String[] args) {
// Names of the mol file
double energy=0.0;
String mname;
String outName;
if (args[0].lastIndexOf(".") < 0) {
mname = args[0]+".out";
outName = args[0]+".fdt";
} else {
mname = args[0];
outName = args[0].substring(0,args[0].lastIndexOf("."))+".fdt";
}
String currLine="XXXX";
int niatms = 0;
double fmult = 1.0;
if (args.length > 1) {
fmult = Double.valueOf(args[1]).doubleValue();
System.out.println("Fmult = "+fmult);
}
BufferedReader buffRead;
BufferedWriter buffWrite;
boolean minimised = true;
String fileType = "Jaguar";
String[] atomtypes;
double[] x;
double[] y;
double[] z;
double[] fx;
double[] fy;
double[] fz;
System.out.println("(c) J M Goodman, 2003");
System.out.println("Cambridge University");
System.out.println("All rights reserved");
System.out.println("");
System.out.println("File name: "+mname);
try {
buffRead = new BufferedReader(new FileReader(new File(mname)));
for (int i = 0; i < 10 ; i++) {
currLine = buffRead.readLine();
if (currLine.indexOf("Jaguar") > -1) fileType = "Jaguar";
if (currLine.indexOf("GAMESS") > -1) fileType = "GAMESS";
}
// Now set minimised and niatms
niatms = 0;
minimised = false;
if (fileType.equalsIgnoreCase("Jaguar")) {
while (currLine.indexOf("Input geometry") < 0) currLine = buffRead.readLine();
currLine = buffRead.readLine();
currLine = buffRead.readLine();
while (currLine.length() > 10) {
currLine = buffRead.readLine();
niatms++;
}
niatms--;
while (currLine.indexOf("final geometry") < 0) currLine = buffRead.readLine();
if (currLine.indexOf("final geometry") >= 0) minimised = true;
} else if (fileType.equalsIgnoreCase("GAMESS")) {
while (currLine.indexOf("COORDINATES (BOHR)") < 0) currLine = buffRead.readLine();
// System.out.println("Found: "+currLine);
currLine = buffRead.readLine();
// System.out.println("Found: "+currLine);
while (currLine.length() > 10) {
currLine = buffRead.readLine();
niatms++;
}
niatms--;
// System.out.println("Number of atoms: "+niatms);
while (currLine.indexOf("LOCATED *****") < 0) currLine = buffRead.readLine();
if (currLine.indexOf("LOCATED *****") >= 0) minimised = true;
// System.out.println("Number of atoms: "+minimised);
}
buffRead.close();
} catch(Exception e) {;}
atomtypes = new String[niatms];
x = new double[niatms];
y = new double[niatms];
z = new double[niatms];
fx = new double[niatms];
fy = new double[niatms];
fz = new double[niatms];
// System.out.println("Number of atoms: "+niatms+" "+minimised);
try {
buffRead = new BufferedReader(new FileReader(new File(mname)));
currLine = "XXXX";
if (fileType.equalsIgnoreCase("Jaguar")) {
if (minimised) while (currLine.indexOf("final geometry") < 0) currLine = buffRead.readLine();
else while (currLine.indexOf("Input geometry") < 0) currLine = buffRead.readLine();
currLine = buffRead.readLine();
currLine = buffRead.readLine();
for (int i = 0; i < niatms; i++) {
currLine = buffRead.readLine();
atomtypes[i] = currLine.substring(0,9);
x[i] = Double.valueOf(currLine.substring(9,25).trim()).doubleValue();
y[i] = Double.valueOf(currLine.substring(25,43).trim()).doubleValue();
z[i] = Double.valueOf(currLine.substring(43).trim()).doubleValue();
// System.out.println(currLine);
}
while (currLine.indexOf("SCF energy:") < 0) currLine = buffRead.readLine();
energy = Double.valueOf(currLine.substring(23,42).trim()).doubleValue();
while (currLine.indexOf("harmonic frequencies") < 0) currLine = buffRead.readLine();
currLine = buffRead.readLine();
while (currLine.indexOf("frequencies") < 0) currLine = buffRead.readLine();
currLine = buffRead.readLine();
// System.out.println("Number of atoms: "+niatms);
// System.out.println(currLine);
for (int i = 0; i < niatms; i++) {
currLine = buffRead.readLine();
if (currLine.indexOf("reduc. mass") > -1) currLine = buffRead.readLine();
fx[i] = Double.valueOf(currLine.substring(12,23).trim()).doubleValue();
System.out.println("x: "+niatms+" "+fx[i]);
currLine = buffRead.readLine();
fy[i] = Double.valueOf(currLine.substring(12,23).trim()).doubleValue();
System.out.println("y: "+niatms+" "+fy[i]);
currLine = buffRead.readLine();
fz[i] = Double.valueOf(currLine.substring(12,23).trim()).doubleValue();
System.out.println("z: "+niatms+" "+fz[i]);
}
} else if (fileType.equalsIgnoreCase("GAMESS")) {
// System.out.println("GAMESS file");
if (minimised) while (currLine.indexOf("LOCATED *****") < 0) currLine = buffRead.readLine();
else while (currLine.indexOf("COORDINATES (BOHR)") < 0) currLine = buffRead.readLine();
// System.out.println("GAMESS file "+minimised);
currLine = buffRead.readLine();
if (minimised) {
currLine = buffRead.readLine();
currLine = buffRead.readLine();
for (int i = 0; i < niatms; i++) {
currLine = buffRead.readLine();
atomtypes[i] = currLine.substring(0,9);
x[i] = Double.valueOf(currLine.substring(17,31).trim()).doubleValue();
y[i] = Double.valueOf(currLine.substring(32,46).trim()).doubleValue();
z[i] = Double.valueOf(currLine.substring(47).trim()).doubleValue();
}
} else {
System.out.println("GAMESS file not minimised");
// System.out.println(currLine);
for (int i = 0; i < niatms; i++) {
currLine = buffRead.readLine();
atomtypes[i] = currLine.substring(0,16);
x[i] = 0.52918*Double.valueOf(currLine.substring(17,33).trim()).doubleValue();
y[i] = 0.52918*Double.valueOf(currLine.substring(34,53).trim()).doubleValue();
z[i] = 0.52918*Double.valueOf(currLine.substring(54).trim()).doubleValue();
}
}
while (currLine.indexOf("FREQUENCY") < 0) currLine = buffRead.readLine();
currLine = buffRead.readLine();
currLine = buffRead.readLine();
// System.out.println("Number of atoms: "+niatms);
// System.out.println(currLine);
for (int i = 0; i < niatms; i++) {
currLine = buffRead.readLine();
fx[i] = Double.valueOf(currLine.substring(21,32).trim()).doubleValue();
// System.out.println("x: "+niatms+" "+fx[i]);
currLine = buffRead.readLine();
fy[i] = Double.valueOf(currLine.substring(21,32).trim()).doubleValue();
// System.out.println("y: "+niatms+" "+fy[i]);
currLine = buffRead.readLine();
fz[i] = Double.valueOf(currLine.substring(21,32).trim()).doubleValue();
// System.out.println("z: "+niatms+" "+fz[i]);
}
}
buffRead.close();
} catch(Exception e) {;}
try {
buffWrite = new BufferedWriter(new FileWriter(new File(outName)));
buffWrite.write("Initial geometry and Energy: "+energy);
buffWrite.newLine();
for (int i = 0; i < niatms; i++) {
buffWrite.write(atomtypes[i]+" "+doubFormat(x[i],10,6)+" "+doubFormat(y[i],10,6)+" "+doubFormat(z[i],10,6));
buffWrite.newLine();
}
buffWrite.newLine();
buffWrite.newLine();
buffWrite.write("changes");
buffWrite.newLine();
for (int i = 0; i < niatms; i++) {
buffWrite.write(atomtypes[i]+" "+doubFormat(fx[i],10,6)+" "+doubFormat(fy[i],10,6)+" "+doubFormat(fz[i],10,6));
buffWrite.newLine();
}
buffWrite.newLine();
buffWrite.newLine();
buffWrite.write("Adding");
buffWrite.newLine();
for (int i = 0; i < niatms; i++) {
buffWrite.write(atomtypes[i]+" "+doubFormat(fmult*fx[i]+x[i],10,6)+" "+doubFormat(fmult*fy[i]+y[i],10,6)+" "+doubFormat(fmult*fz[i]+z[i],10,6));
buffWrite.newLine();
}
buffWrite.newLine();
buffWrite.newLine();
buffWrite.write("Subtracting");
buffWrite.newLine();
for (int i = 0; i < niatms; i++) {
buffWrite.write(atomtypes[i]+" "+doubFormat(-fmult*fx[i]+x[i],10,6)+" "+doubFormat(-fmult*fy[i]+y[i],10,6)+" "+doubFormat(-fmult*fz[i]+z[i],10,6));
buffWrite.newLine();
}
buffWrite.close();
} catch(Exception e) {;}
}
static String doubFormat(double number, int length, int decPlace) {
// System.out.println(number);
String temp = " 0.000000000000000";
String temp2 = Double.toString(number);
int k = temp2.indexOf("E");
if (k < 0) {
temp = " "+Double.toString(number)+"0000000000";
int j = temp.indexOf('.');
temp = temp.substring(0,j+decPlace+1);
int i = temp.length();
return temp.substring(i-length);
} else {
temp2 = temp2.substring(k);
int m = temp2.length();
if (m > decPlace) {
temp = " 0.000000000000000";
int j = temp.indexOf('.');
temp = temp.substring(0,j+decPlace+1);
} else {
temp = " "+Double.toString(number).substring(0,k)+"0000000000000000";
int j = temp.indexOf('.');
temp = temp.substring(0,j+decPlace+1-m)+temp2;
}
int i = temp.length();
return temp.substring(i-length);
}
}
}
© 2003 J M Goodman, Cambridge 
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