/**
* <scalar>******************************************</scalar> <scalar>Gaussian 03:
* AM64L-G03RevE.01 11-Sep-2007</scalar> <scalar>30-Mar-2009</scalar>
* <scalar>******************************************</scalar>
*/
private CMLModule readVersion() {
CMLModule module = new CMLModule();
module.setDictRef("gaussian:version");
String version = "";
while (true) {
readLine();
if (line.trim().startsWith("*****************")) {
// LOG.debug("read VERSION to: "+line);
break;
}
version += line;
}
CMLScalar scalar = new CMLScalar(version);
module.appendChild(scalar);
return module;
}
/**
* <scalar>----------------------------------------------------------------------</scalar>
* <scalar>#p uB971/6-311+G(d,p) opt=(Tight, NewEstmFC, MaxCyc = 200) freq #GFInp</scalar>
* <scalar>ut Population=Regular #Integral(Grid=UltraFine) Guess=Mix NoSymmetry</scalar>
* <scalar>----------------------------------------------------------------------</scalar>
*/
private CMLModule readParams() {
CMLModule module = new CMLModule();
module.setDictRef("gaussian:params");
String params = "";
while (true) {
readLine();
if (line.trim().startsWith("------------------")) {
// LOG.debug("read PARAMS to: "+line);
break;
}
params += line;
}
CMLScalar scalar = new CMLScalar(params);
module.appendChild(scalar);
return module;
}
/**
* <scalar>1/6=200,7=10,10=7,14=-1,18=20,26=3,38=1/1,3;</scalar>
* <scalar>2/9=110,15=1,17=6,18=5,40=1/2;</scalar>
* <scalar>3/5=4,6=6,7=111,11=2,16=1,24=10,25=1,30=1,74=-20,75=5/1,2,3;</scalar>
* <scalar>4/7=2,9=2,13=1/1;</scalar> <scalar>5/5=2,38=5/2;</scalar> <scalar>6/28=1/1;</scalar>
* <scalar>7/29=1,30=1/1,2,3,16;</scalar> <scalar>1/6=200,10=7,14=-1,18=20/3(3);</scalar>
* <scalar>2/9=110,15=1/2;</scalar> <scalar>6/19=2,28=1/1;</scalar> <scalar>99//99;</scalar>
* <scalar>2/9=110,15=1/2;</scalar>
* <scalar>3/5=4,6=6,7=111,11=2,16=1,25=1,30=1,74=-20,75=5/1,2,3;</scalar>
* <scalar>4/5=5,7=2,9=2,16=3/1;</scalar> <scalar>5/5=2,38=5/2;</scalar>
* <scalar>7/30=1/1,2,3,16;</scalar> <scalar>1/6=200,14=-1,18=20/3(-5);</scalar>
* <scalar>2/9=110,15=1/2;</scalar> <scalar>6/19=2,28=1/1;</scalar> <scalar>99/9=1/99;</scalar>
*
* @return
*/
private CMLElement readLinkCommands() {
CMLModule cmlModule = new CMLModule();
cmlModule.setDictRef("gaussian:links");
while (true) {
readLine();
Matcher matcher = LINK_PATTERN.matcher(line);
if (!matcher.matches()) {
line_num--;
break;
}
String overlayS = matcher.group(1);
String pS = matcher.group(2);
String[] params = (pS == null) ? null : pS.split(CMLConstants.S_COMMA);
String jumpS = matcher.group(7);
String sub = matcher.group(4);
String[] subOver = sub.split(CMLConstants.S_COMMA);
for (String s : subOver) {
s = (s.length() == 2) ? s : "0" + s;
String ss = overlayS + s;
CMLModule overlayModule = new CMLModule();
cmlModule.appendChild(overlayModule);
overlayModule.setTitle(overlayS);
overlayModule.setDictRef("gaussian:link" + ss);
if (params != null) {
for (String param : params) {
String[] ll = param.split(CMLConstants.S_EQUALS);
CMLParameter parameter = new CMLParameter();
parameter.setDictRef("gaussian:p" + ll[0]);
parameter.setCMLValue(ll[1]);
overlayModule.appendChild(parameter);
}
}
if (jumpS != null) {
CMLParameter parameter = new CMLParameter();
parameter.setDictRef("gaussian:jump");
parameter.setCMLValue(jumpS);
overlayModule.appendChild(parameter);
}
}
}
return cmlModule;
}