org.openscience.cdk.io.program.GaussianInputWriter Maven / Gradle / Ivy
/* Copyright (C) 2003-2008 Egon Willighagen
*
* Contact: [email protected]
*
* This library is free software; you can redistribute it and/or
* modify it under the terms of the GNU Lesser General Public
* License as published by the Free Software Foundation; either
* version 2.1 of the License, or (at your option) any later version.
*
* This library is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
* Lesser General Public License for more details.
*
* You should have received a copy of the GNU Lesser General Public
* License along with this library; if not, write to the Free Software
* Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA.
*/
package org.openscience.cdk.io.program;
import java.io.BufferedWriter;
import java.io.IOException;
import java.io.OutputStream;
import java.io.OutputStreamWriter;
import java.io.StringWriter;
import java.io.Writer;
import java.util.ArrayList;
import java.util.Iterator;
import java.util.List;
import javax.vecmath.Point3d;
import org.openscience.cdk.exception.CDKException;
import org.openscience.cdk.interfaces.IAtom;
import org.openscience.cdk.interfaces.IAtomContainer;
import org.openscience.cdk.interfaces.IChemObject;
import org.openscience.cdk.io.DefaultChemObjectWriter;
import org.openscience.cdk.io.formats.GaussianInputFormat;
import org.openscience.cdk.io.formats.IResourceFormat;
import org.openscience.cdk.io.setting.BooleanIOSetting;
import org.openscience.cdk.io.setting.IOSetting;
import org.openscience.cdk.io.setting.IntegerIOSetting;
import org.openscience.cdk.io.setting.OptionIOSetting;
import org.openscience.cdk.io.setting.StringIOSetting;
/**
* File writer thats generates input files for Gaussian calculation
* jobs. It was tested with Gaussian98.
*
* @cdk.module io
* @cdk.githash
*
* @author Egon Willighagen
*
* @cdk.keyword Gaussian (tm), input file
*/
public class GaussianInputWriter extends DefaultChemObjectWriter {
static BufferedWriter writer;
IOSetting method;
IOSetting basis;
IOSetting comment;
IOSetting command;
IOSetting memory;
BooleanIOSetting shell;
IntegerIOSetting proccount;
BooleanIOSetting usecheckpoint;
/**
* Constructs a new writer that produces input files to run a
* Gaussian QM job.
*/
public GaussianInputWriter(Writer out) {
try {
if (out instanceof BufferedWriter) {
writer = (BufferedWriter) out;
} else {
writer = new BufferedWriter(out);
}
} catch (Exception exc) {
}
initIOSettings();
}
public GaussianInputWriter(OutputStream output) {
this(new OutputStreamWriter(output));
}
public GaussianInputWriter() {
this(new StringWriter());
}
@Override
public IResourceFormat getFormat() {
return GaussianInputFormat.getInstance();
}
@Override
public void setWriter(Writer out) throws CDKException {
if (out instanceof BufferedWriter) {
writer = (BufferedWriter) out;
} else {
writer = new BufferedWriter(out);
}
}
@Override
public void setWriter(OutputStream output) throws CDKException {
setWriter(new OutputStreamWriter(output));
}
@Override
public void close() throws IOException {
writer.close();
}
@Override
public boolean accepts(Class classObject) {
return IAtomContainer.class.isAssignableFrom(classObject);
}
@Override
public void write(IChemObject object) throws CDKException {
if (object instanceof IAtomContainer) {
try {
writeMolecule((IAtomContainer) object);
} catch (Exception ex) {
throw new CDKException("Error while writing Gaussian input file: " + ex.getMessage(), ex);
}
} else {
throw new CDKException("GaussianInputWriter only supports output of Molecule classes.");
}
}
/**
* Writes a molecule for input for Gaussian.
*/
public void writeMolecule(IAtomContainer mol) throws IOException {
customizeJob();
// write extra statements
if (proccount.getSettingValue() > 1) {
writer.write("%nprocl=" + proccount.getSettingValue());
writer.newLine();
}
if (!memory.getSetting().equals("unset")) {
writer.write("%Mem=" + memory.getSetting());
writer.newLine();
}
if (usecheckpoint.isSet()) {
if (mol.getID() != null && mol.getID().length() > 0) {
writer.write("%chk=" + mol.getID() + ".chk");
} else {
// force different file names
writer.write("%chk=" + System.currentTimeMillis() + ".chk");
}
writer.newLine();
}
// write the command line
writer.write("# " + method.getSetting() + "/" + basis.getSetting() + " ");
String commandString = command.getSetting();
if (commandString.equals("energy calculation")) {
// ok, no special command needed
} else if (commandString.equals("geometry optimization")) {
writer.write("opt");
} else if (commandString.equals("IR frequency calculation")) {
writer.write("freq");
} else if (commandString.equals("IR frequency calculation (with Raman)")) {
writer.write("freq=noraman");
} else {
// assume that user knows what he's doing
writer.write(commandString);
}
writer.newLine();
// next line is empty
writer.newLine();
// next line is comment
writer.write(comment.getSetting());
writer.newLine();
// next line is empty
writer.newLine();
/*
* next line contains two digits the first is the total charge the
* second is boolean indicating: 0 = open shell 1 = closed shell
*/
writer.write("0 "); // FIXME: should write total charge of molecule
if (shell.isSet()) {
writer.write("0");
} else {
writer.write("1");
}
writer.newLine();
// then come all the atoms.
// Loop through the atoms and write them out:
Iterator atoms = mol.atoms().iterator();
while (atoms.hasNext()) {
IAtom a = atoms.next();
String st = a.getSymbol();
// export Eucledian coordinates (indicated by the 0)
st = st + " 0 ";
// export the 3D coordinates
Point3d p3 = a.getPoint3d();
if (p3 != null) {
st = st + new Double(p3.x).toString() + " " + new Double(p3.y).toString() + " "
+ new Double(p3.z).toString();
}
writer.write(st, 0, st.length());
writer.newLine();
}
// G98 expects an empty line at the end
writer.newLine();
}
private void initIOSettings() {
List basisOptions = new ArrayList();
basisOptions.add("6-31g");
basisOptions.add("6-31g*");
basisOptions.add("6-31g(d)");
basisOptions.add("6-311g");
basisOptions.add("6-311+g**");
basis = new OptionIOSetting("Basis", IOSetting.Importance.MEDIUM, "Which basis set do you want to use?",
basisOptions, "6-31g");
List methodOptions = new ArrayList();
methodOptions.add("rb3lyp");
methodOptions.add("b3lyp");
methodOptions.add("rhf");
method = new OptionIOSetting("Method", IOSetting.Importance.MEDIUM, "Which method do you want to use?",
methodOptions, "b3lyp");
List commandOptions = new ArrayList();
commandOptions.add("energy calculation");
commandOptions.add("geometry optimization");
commandOptions.add("IR frequency calculation");
commandOptions.add("IR frequency calculation (with Raman)");
command = addSetting(new OptionIOSetting("Command", IOSetting.Importance.HIGH,
"What kind of job do you want to perform?", commandOptions, "energy calculation"));
comment = addSetting(new StringIOSetting("Comment", IOSetting.Importance.LOW,
"What comment should be put in the file?", "Created with CDK (http://cdk.sf.net/)"));
memory = addSetting(new StringIOSetting("Memory", IOSetting.Importance.LOW,
"How much memory do you want to use?", "unset"));
shell = addSetting(new BooleanIOSetting("OpenShell", IOSetting.Importance.MEDIUM,
"Should the calculation be open shell?", "false"));
proccount = addSetting(new IntegerIOSetting("ProcessorCount", IOSetting.Importance.LOW,
"How many processors should be used by Gaussian?", "1"));
usecheckpoint = new BooleanIOSetting("UseCheckPointFile", IOSetting.Importance.LOW,
"Should a check point file be saved?", "false");
}
private void customizeJob() {
for (IOSetting setting : getSettings()) {
fireIOSettingQuestion(setting);
}
}
}
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