/* $RCSfile$
* $Author: hansonr $
* $Date: 2006-09-16 14:11:08 -0500 (Sat, 16 Sep 2006) $
* $Revision: 5569 $
*
* Copyright (C) 2003-2005 Miguel, Jmol Development, www.jmol.org
*
* Contact: jmol-developers@lists.sf.net
*
* 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.
*/
/*
* US modifications by Albert DeFusco - adefusco and Bob Hanson 12/2/2008
*
*/
package org.jmol.adapter.readers.quantum;
import java.util.ArrayList;
import javax.vecmath.Vector3f;
import org.jmol.adapter.smarter.Atom;
import org.jmol.util.Logger;
public class GamessUSReader extends GamessReader {
/*
------------------
MOLECULAR ORBITALS
------------------
------------
EIGENVECTORS
------------
1 2 3 4 5
-79.9156 -20.4669 -20.4579 -20.4496 -20.4419
A A A A A
1 C 1 S -0.000003 -0.000029 -0.000004 0.000011 0.000016
2 C 1 S -0.000009 0.000140 0.000001 0.000057 0.000065
3 C 1 X 0.000007 -0.000241 -0.000022 -0.000010 -0.000061
4 C 1 Y -0.000008 0.000017 -0.000027 -0.000010 0.000024
5 C 1 Z 0.000007 0.000313 0.000009 -0.000002 -0.000001
6 C 1 S 0.000049 0.000875 -0.000164 -0.000521 -0.000440
7 C 1 X -0.000066 0.000161 0.000125 0.000034 0.000406
8 C 1 Y 0.000042 0.000195 -0.000165 -0.000254 -0.000573
9 C 1 Z 0.000003 0.000045 0.000052 0.000112 -0.000129
10 C 1 XX -0.000010 0.000010 -0.000040 0.000019 0.000045
11 C 1 YY -0.000010 -0.000031 0.000000 -0.000003 0.000019
...
6 7 8 9 10
-20.4354 -20.4324 -20.3459 -20.3360 -11.2242
A A A A A
1 C 1 S 0.000000 -0.000001 0.000001 0.000000 0.008876
2 C 1 S -0.000003 0.000002 0.000003 0.000002 0.000370
...
TOTAL NUMBER OF BASIS SET SHELLS = 101
*/
/**
* @return true if need to read new line
* @throws Exception
*
*/
protected boolean checkLine() throws Exception {
boolean isBohr;
if (line.indexOf("BASIS OPTIONS") >= 0){
readBasisInfo();
return true;
}
if (line.indexOf("$CONTRL OPTIONS") >= 0){
readControlInfo();
return true;
}
if (line.indexOf("ATOMIC BASIS SET") >= 0) {
readGaussianBasis("SHELL TYPE", "TOTAL");
return false;
}
if ((isBohr = line.indexOf("COORDINATES (BOHR)") >= 0)
|| line.indexOf("COORDINATES OF ALL ATOMS ARE (ANGS)") >= 0) {
if (!doGetModel(++modelNumber))
return checkLastModel();
atomNames = new ArrayList();
if (isBohr)
readAtomsInBohrCoordinates();
else
readAtomsInAngstromCoordinates();
return true;
}
if (!doProcessLines)
return true;
if (line.indexOf("FREQUENCIES IN CM") >= 0) {
readFrequencies();
return true;
}
if (line.indexOf("SUMMARY OF THE EFFECTIVE FRAGMENT") >= 0) {
// We have EFP and we're not afraid to use it!!
// it would be nice is this information was closer to the ab initio
// molecule
readEFPInBohrCoordinates();
return false;
}
if (line.indexOf(" TOTAL MULLIKEN AND LOWDIN ATOMIC POPULATIONS") >= 0) {
readPartialCharges();
return false;
}
if (line.indexOf("ELECTROSTATIC MOMENTS")>=0){
readDipoleMoment();
return true;
}
if (line.indexOf("- ALPHA SET -") >= 0)
alphaBeta = "alpha";
else if (line.indexOf("- BETA SET -") >= 0)
alphaBeta = "beta";
else if (line.indexOf(" EIGENVECTORS") >= 0
|| line.indexOf(" INITIAL GUESS ORBITALS") >= 0
|| line.indexOf(" MCSCF OPTIMIZED ORBITALS") >= 0
|| line.indexOf(" MCSCF NATURAL ORBITALS") >= 0
|| line.indexOf(" MOLECULAR ORBITALS") >= 0
&& line
.indexOf(" MOLECULAR ORBITALS LOCALIZED BY THE POPULATION METHOD") < 0) {
if (!filterMO())
return true;
// energies and possibly symmetries
readMolecularOrbitals(HEADER_GAMESS_ORIGINAL);
return false;
}
if (line.indexOf("EDMISTON-RUEDENBERG ENERGY LOCALIZED ORBITALS") >= 0
|| line.indexOf(" THE PIPEK-MEZEY POPULATION LOCALIZED ORBITALS ARE") >= 0) {
if (!filterMO())
return true;
readMolecularOrbitals(HEADER_NONE);
return false;
}
if (line.indexOf(" NATURAL ORBITALS IN ATOMIC ORBITAL BASIS") >= 0) {
// the for mat of the next orbitals can change depending on the
// cistep used. This works for ALDET and GUGA
// BH to AD: but the GUGA file delivered has only energies?
if (!filterMO())
return true;
readMolecularOrbitals(HEADER_GAMESS_OCCUPANCIES);
return false;
}
return checkNboLine();
}
protected void readMolecularOrbitals(int headerType) throws Exception {
setCalculationType();
super.readMolecularOrbitals(headerType);
}
/*
for H2ORHF, the Z entries are nuclear positions
MULTIPOLE COORDINATES, ELECTRONIC AND NUCLEAR CHARGES
X Y Z ELEC. NUC.
ZO1 -7.7339870636 0.7855024013 0.0607735878 8.00000 0.0
ZH2 -6.3592068574 1.8865489098 -0.2204029069 1.00000 0.0
ZH3 -8.0979273324 0.8550163890 1.8055083920 1.00000 0.0
O1 -7.7339870636 0.7855024013 0.0607735878 -8.21083 0.0
H2 -6.3592068574 1.8865489098 -0.2204029069 -0.55665 0.0
H3 -8.0979273324 0.8550163890 1.8055083920 -0.55665 0.0
B12 -7.0465971979 1.3360253807 -0.0798150033 -0.33793 0.0
B13 -7.9159574354 0.8202591203 0.9331406462 -0.33793 0.0
for H2ODFT
MULTIPOLE COORDINATES, ELECTRONIC AND NUCLEAR CHARGES
X Y Z ELEC. NUC.
O1 6.7090100309 -3.9975560003 -0.0215951332 -8.22458 8.0
H2 7.4569069150 -4.5350351179 -1.5490605828 -0.57906 1.0
H3 7.1548619721 -2.2838340456 0.1923145656 -0.57906 1.0
B12 7.0829581926 -4.2662958353 -0.7853275496 -0.30866 0.0
B13 6.9319357212 -3.1406952991 0.0853600246 -0.30866 0.0
*/
protected void readEFPInBohrCoordinates() throws Exception {
//it's really too bad that the EFP information is nowhere near
//the ab initio molecule for single-point runs.
int atomCountInFirstModel = atomSetCollection.getAtomCount();
//should only contain the $DATA card
discardLinesUntilContains("MULTIPOLE COORDINATES");
readLine(); // blank line
readLine(); // X Y Z ELEC. NUC.
//at least for FRAGNAME=H2ORHF, the atoms come out as ZO1, ZH2, ZH3
//Z stands for nuclear position.
while (readLine() != null && line.length() >= 72) {
String atomName = line.substring(1, 2);
//Z is perhaps not officially deprecated, but the newer
//H2ODFT potential doesn't use it.
//It does however put the nuclear charge in the last column
if (atomName.charAt(0) == 'Z')
atomName = line.substring(2, 3);
else if (parseFloat(line, 67, 73) == 0)
continue;
float x = parseFloat(line, 8, 25);
float y = parseFloat(line, 25, 40);
float z = parseFloat(line, 40, 56);
if (Float.isNaN(x) || Float.isNaN(y) || Float.isNaN(z))
break;
Atom atom = atomSetCollection.addNewAtom();
atom.atomName = atomName + (++atomCountInFirstModel);
atom.set(x, y, z);
atom.scale(ANGSTROMS_PER_BOHR);
atomNames.add(atomName);
}
}
protected void readAtomsInBohrCoordinates() throws Exception {
/*
ATOM ATOMIC COORDINATES (BOHR)
CHARGE X Y Z
C 6.0 3.9770911639 -2.7036584676 -0.3453920672
0 1 2 3 4 5 6 7
01234567890123456789012345678901234567890123456789012345678901234567890123456789
*/
readLine(); // discard one line
String atomName;
atomSetCollection.newAtomSet();
int n = 0;
while (readLine() != null
&& (atomName = parseToken(line, 1, 11)) != null) {
float x = parseFloat(line, 17, 37);
float y = parseFloat(line, 37, 57);
float z = parseFloat(line, 57, 77);
if (Float.isNaN(x) || Float.isNaN(y) || Float.isNaN(z))
break;
Atom atom = atomSetCollection.addNewAtom();
atom.elementSymbol = getElementSymbol(parseInt(line.substring(11, 14)));
atom.atomName = atom.elementSymbol + (++n);
atom.set(x, y, z);
atom.scale(ANGSTROMS_PER_BOHR);
atomNames.add(atomName);
}
}
private void readAtomsInAngstromCoordinates() throws Exception {
readLine();
readLine(); // discard two lines
String atomName;
atomSetCollection.newAtomSet();
/*
COORDINATES OF ALL ATOMS ARE (ANGS)
ATOM CHARGE X Y Z
------------------------------------------------------------
C 6.0 2.1045861621 -1.4307145508 -0.1827736240
0 1 2 3 4 5 6
0123456789012345678901234567890123456789012345678901234567890
*/
int n = 0;
while (readLine() != null
&& (atomName = parseToken(line, 1, 11)) != null) {
float x = parseFloat(line, 16, 31);
float y = parseFloat(line, 31, 46);
float z = parseFloat(line, 46, 61);
if (Float.isNaN(x) || Float.isNaN(y) || Float.isNaN(z))
break;
Atom atom = atomSetCollection.addNewAtom();
atom.set(x, y, z);
atom.elementSymbol = getElementSymbol(parseInt(line.substring(11, 14)));
atom.atomName = atom.elementSymbol + (++n);
atomNames.add(atomName);
}
/*
During optimization, this will immediately appear after the
ab initio molecule
COORDINATES OF FRAGMENT MULTIPOLE CENTERS (ANGS)
MULTIPOLE NAME X Y Z
------------------------------------------------------------
FRAGNAME=H2ORHF
ZO1 -4.1459482636 0.4271933699 0.0417242924
ZH2 -3.4514529072 1.0596960013 -0.0504444399
ZH3 -4.5252917848 0.5632659571 0.8952236761
or for H2ODFT
COORDINATES OF FRAGMENT MULTIPOLE CENTERS (ANGS)
MULTIPOLE NAME X Y Z
------------------------------------------------------------
FRAGNAME=H2ODFT
O1 3.5571448937 -2.1158335714 -0.0044768463
H2 3.9520351868 -2.4002052098 -0.8132245708
H3 3.7885802785 -1.2074436330 0.1057222304
*/
// Now is the time to read Effective Fragments (EFP)
if (line.indexOf("COORDINATES OF FRAGMENT MULTIPOLE CENTERS (ANGS)") >= 0) {
readLine(); // MULTIPONE NAME X ...
readLine(); // ------------------------ ...
readLine(); // FRAGNAME=
//at least for FRAGNAME=H2ORHF, the atoms come out as ZO1, ZH2, ZH3
while (readLine() != null
&& (atomName = parseToken(line, 1, 2)) != null) {
if (parseToken(line,1,2).equals("Z")) //Z means nuclear position
atomName = parseToken(line, 2, 3);
else if (parseToken(line,1,9).equals("FRAGNAME"))//Z is a deprecated requirement
continue;
else
atomName = parseToken(line, 1, 2);
float x = parseFloat(line, 16, 31);
float y = parseFloat(line, 31, 46);
float z = parseFloat(line, 46, 61);
if (Float.isNaN(x) || Float.isNaN(y) || Float.isNaN(z))
break;
Atom atom = atomSetCollection.addNewAtom();
atom.atomName = atomName + (++n);
atom.set(x, y, z);
atomNames.add(atomName);
}
}
}
/*
*
ATOMIC BASIS SET
----------------
THE CONTRACTED PRIMITIVE FUNCTIONS HAVE BEEN UNNORMALIZED
THE CONTRACTED BASIS FUNCTIONS ARE NOW NORMALIZED TO UNITY
SHELL TYPE PRIMITIVE EXPONENT CONTRACTION COEFFICIENTS
C
1 S 1 172.2560000 .061766907377
1 S 2 25.9109000 .358794042852
1 S 3 5.5333500 .700713083689
2 L 4 3.6649800 -.395895162119 .236459946619
2 L 5 .7705450 1.215834355681 .860618805716
OR:
SHELL TYPE PRIM EXPONENT CONTRACTION COEFFICIENTS
C
1 S 1 71.616837 2.707814 ( 0.154329)
1 S 2 13.045096 2.618880 ( 0.535328)
1 S 3 3.530512 0.816191 ( 0.444635)
2 L 4 2.941249 -0.160017 ( -0.099967) 0.856045 ( 0.155916)
2 L 5 0.683483 0.214036 ( 0.399513) 0.538304 ( 0.607684)
2 L 6 0.222290 0.161536 ( 0.700115) 0.085276 ( 0.391957)
*/
protected String fixShellTag(String tag) {
return tag;
}
/*
TOTAL MULLIKEN AND LOWDIN ATOMIC POPULATIONS
ATOM MULL.POP. CHARGE LOW.POP. CHARGE
1 O 8.000000 0.000000 8.000000 0.000000
2 O 8.000000 0.000000 8.000000 0.000000
*/
/**
* @throws Exception
*/
void readPartialCharges() throws Exception {
String tokens[]=null;
String searchstr = (checkFilter("CHARGE=LOW") ? "LOW.POP."
: "MULL.POP.");
while (readLine() != null && ("".equals(line.trim())||line.indexOf("ATOM") >= 0)) {
tokens = getTokens();
}
int poploc = 0;
for (; ++poploc < tokens.length; )
if (searchstr.equals(tokens[poploc]))
break;
if (++poploc >= tokens.length || !"CHARGE".equals(tokens[poploc++]))
return; // Not as expected don't read
Atom[] atoms = atomSetCollection.getAtoms();
int startAtom = atomSetCollection.getLastAtomSetAtomIndex();
int endAtom = atomSetCollection.getAtomCount();
for (int i = startAtom; i < endAtom && readLine() != null; ++i)
atoms[i].partialCharge = parseFloat(getTokens(prevline)[poploc]);
}
/*
---------------------
ELECTROSTATIC MOMENTS
---------------------
POINT 1 X Y Z (BOHR) CHARGE
0.000000 0.000000 -0.020735 0.00 (A.U.)
DX DY DZ /D/ (DEBYE)
0.000000 0.000000 -1.449162 1.449162
*/
void readDipoleMoment() throws Exception {
String tokens[] = null;
readLine();
while (line != null && ("".equals(line.trim()) || line.indexOf("DX") < 0)) {
readLine();
}
tokens = getTokens(line);
if (tokens.length != 5)
return;
if ("DX".equals(tokens[0]) && "DY".equals(tokens[1])
&& "DZ".equals(tokens[2])) {
tokens = getTokens(readLine());
Vector3f dipole = new Vector3f(parseFloat(tokens[0]),
parseFloat(tokens[1]), parseFloat(tokens[2]));
Logger.info("Molecular dipole for model "
+ atomSetCollection.getAtomSetCount() + " = " + dipole);
atomSetCollection.setAtomSetAuxiliaryInfo("dipole", dipole);
}
}
}