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);
setAtomCoord(atom, x * ANGSTROMS_PER_BOHR, y * ANGSTROMS_PER_BOHR, z * ANGSTROMS_PER_BOHR);
atomNames.add(atomName);
}
}
@Override
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);
setAtomCoord(atom, x * ANGSTROMS_PER_BOHR, y * ANGSTROMS_PER_BOHR, z * ANGSTROMS_PER_BOHR);
atomNames.add(atomName);
}
}
private void readAtoms() throws Exception {
// format (4X,I4,4X,F10.8,3X,F10.8,3X,F10.8)
readLine();
while (line != null && (line.indexOf("ATOM") == 0 || !doSymmetry && line.indexOf(":") == 8)) {
int thisAtom = atomSetCollection.getAtomCount();
addAtom();
if (readLine().indexOf("MULT=") == 10)
for (int i = parseInt(line.substring(15, 18)); --i >= 0; ) {
readLine();
if (!doSymmetry) addAtom();
}
// format (A10,5X,I5,5X,F10.8,5X,F10.5,5X,F5.2)
String atomName = line.substring(0, 10);
String sym = atomName.substring(0, 2).trim();
if (sym.length() == 2 && Character.isDigit(sym.charAt(1))) sym = sym.substring(0, 1);
atomName = TextFormat.simpleReplace(atomName, " ", "");
int n = 0;
for (int i = atomSetCollection.getAtomCount(); --i >= thisAtom; ) {
Atom atom = atomSetCollection.getAtom(i);
atom.elementSymbol = sym;
atom.atomName = atomName + "_" + (n++);
}
while (readLine() != null && line.indexOf("ATOM") < 0 && line.indexOf("SYMMETRY") < 0) {}
}
// return with "SYMMETRY" line in buffer
}
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();
setAtomCoord(atom, 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);
setAtomCoord(atom, x, y, z);
atomNames.add(atomName);
}
}
}
