//returns a hop based on the information on the line
Hop getHopFromLine(string line){
Hop hop = createHop(-1, -1, -1);
char *tokens;
char *charLine = (char *)malloc(sizeof(char) * line.size());
strcpy(charLine, line.c_str());
tokens = strtok(charLine, " ");
int tokenNumber = 0;
while(tokens != NULL){
switch(tokenNumber){
case 0:
hop.atom1 = atoi(tokens);
break;
case 1:
hop.atom2 = atoi(tokens);
break;
case 2:
hop.hop = atoi(tokens);
break;
}
tokens = strtok(NULL, " ");
tokenNumber++;
}
return hop;
}
Hop
RouteParser::createHop(stringref str)
{
if (str.empty()) {
return Hop().addDirective(createErrorDirective("Failed to parse empty string."));
}
size_t len = str.size();
if (len > 1 && str[0] == '?') {
Hop hop = createHop(str.substr(1));
hop.setIgnoreResult(true);
return hop;
}
if (len > 4 && str.substr(0, 4) == "tcp/") {
IHopDirective::SP tcp = createTcpDirective(str.substr(4));
if (tcp.get() != nullptr) {
return Hop().addDirective(tcp);
}
}
if (len > 6 && str.substr(0, 6) == "route:") {
return Hop().addDirective(createRouteDirective(str.substr(6)));
}
Hop ret;
for (size_t from = 0, at = 0, depth = 0; at <= len; ++at) {
if (at == len || (depth == 0 && str[at] == '/')) {
if (depth > 0) {
return Hop().addDirective(createErrorDirective(
"Unexpected token '': syntax error"));
}
ret.addDirective(createDirective(str.substr(from, at - from)));
from = at + 1;
} else if (isWhitespace(str[at]) && depth == 0) {
return Hop().addDirective(createErrorDirective(
vespalib::make_string(
"Failed to completely parse '%s'.",
vespalib::string(str).c_str())));
} else if (str[at] == '[') {
++depth;
} else if (str[at] == ']') {
if (depth == 0) {
return Hop().addDirective(createErrorDirective(
"Unexpected token ']': syntax error"));
}
--depth;
}
}
return ret;
}
Route
RouteParser::createRoute(stringref str)
{
Route ret;
for (size_t from = 0, at = 0, depth = 0; at <= str.size(); ++at) {
if (at == str.size() || (depth == 0 && isWhitespace(str[at]))) {
if (from < at - 1) {
Hop hop = createHop(str.substr(from, at - from));
if (hop.hasDirectives() &&
hop.getDirective(0)->getType() == IHopDirective::TYPE_ERROR)
{
return std::move(Route().addHop(std::move(hop)));
}
ret.addHop(std::move(hop));
}
from = at + 1;
} else if (str[at] == '[') {
++depth;
} else if (str[at] == ']') {
--depth;
}
}
return ret;
}
Molecule createMeshZMolecules(Opls_Scan *scanner)
{
//1 S 200 0 0 0.000000 0 0.000000 0 0.000000 0
Atom atom1=scanner->getAtom("200");
atom1.id=1;
// 2 DUM -1 0 1 0.500000 0 0.000000 0 0.000000 0
Atom atom2=createAtom(2,-1,-1,-1,-1,-1,-1,NULL);
Bond bond2=createBond(2,1,0.5,false);
//3 DUM -1 0 2 0.500000 1 90.000000 0 0.000000 0
Atom atom3=createAtom(3,-1,-1,-1,-1,-1,-1,NULL);
Bond bond3=createBond(3,2,0.5,false);
Angle angle3=createAngle(3,1,90,false);
//4 hH 204 0 1 1.336532 2 90.000000 3 180.000000 0
Atom atom4=scanner->getAtom("204");
atom4.id=4;
Bond bond4=createBond(4,1,1.336532,true);
Angle angle4=createAngle(4,2,90,false);
Dihedral dihed4=createDihedral(4,3,180,false);
//5 C 217 0 1 1.811119 4 96.401770 2 180.000000 0
Atom atom5=scanner->getAtom("217");
atom5.id=5;
Bond bond5=createBond(5,1,1.811119,true);
Angle angle5=createAngle(5,4,96.401770,true);
Dihedral dihed5=createDihedral(5,2,180,false);
//6 HC 140 0 5 1.090187 1 110.255589 4 179.999947 0
Atom atom6=scanner->getAtom("140");
atom6.id=6;
Bond bond6=createBond(6,5,1.090187,true);
Angle angle6=createAngle(6,1,110.255589,true);
Dihedral dihed6=createDihedral(6,4,179.999947,true);
//7 HC 140 0 5 1.090135 6 108.527646 1 121.053891 0
Atom atom7=scanner->getAtom("140");
atom7.id=7;
Bond bond7=createBond(7,5,1.090135,true);
Angle angle7=createAngle(7,6,108.527646,true);
Dihedral dihed7=createDihedral(7,1,121.053891,true);
//8 HC 140 0 5 1.090135 6 108.527646 1 238.946114 0
Atom atom8=scanner->getAtom("140");
atom8.id=8;
Bond bond8=createBond(8,5,1.090135,true);
Angle angle8=createAngle(8,6,108.527646,true);
Dihedral dihed8=createDihedral(8,1,238.946114,true);
/* HOPS and BONDS Diagram of Mesh.z
// 1--2--3
// |\
// | \
// 4 5
// /|\
// / | \
// 6 7 8
*/
//All hops that have a hop distance >= 3
Hop hop1= createHop(2,6,3);
Hop hop2= createHop(2,7,3);
Hop hop3= createHop(2,8,3);
Hop hop4= createHop(3,4,3);
Hop hop5= createHop(3,5,3);
Hop hop6= createHop(3,6,4);
Hop hop7= createHop(3,7,4);
Hop hop8= createHop(3,8,4);
Hop hop9= createHop(4,6,3);
Hop hop10= createHop(4,7,3);
Hop hop11= createHop(4,8,3);
Atom *atomPtr = new Atom[8];
Bond *bondPtr = new Bond[7];
Angle *anglePtr = new Angle[6];
Dihedral *dihedPtr = new Dihedral[5];
Hop *hopPtr = new Hop[11];
atomPtr[0]=atom1; atomPtr[1]=atom2; atomPtr[2]=atom3; atomPtr[3]=atom4; atomPtr[4]=atom5; atomPtr[5]=atom6; atomPtr[6]=atom7; atomPtr[7]=atom8;
bondPtr[0]=bond2; bondPtr[1]=bond3; bondPtr[2]=bond4; bondPtr[3]=bond5; bondPtr[4]=bond6; bondPtr[5]=bond7; bondPtr[6]=bond8;
anglePtr[0]=angle3; anglePtr[1]=angle4; anglePtr[2]=angle5; anglePtr[3]=angle6; anglePtr[4]=angle7; anglePtr[5]=angle8;
dihedPtr[0]=dihed4; dihedPtr[1]=dihed5; dihedPtr[2]=dihed6; dihedPtr[3]=dihed7; dihedPtr[4]=dihed8;
hopPtr[0]=hop1; hopPtr[1]=hop2; hopPtr[2]=hop3; hopPtr[3]=hop4; hopPtr[4]=hop5; hopPtr[5]=hop6; hopPtr[6]=hop7; hopPtr[7]=hop8; hopPtr[8]=hop9;
hopPtr[9]=hop10; hopPtr[10]=hop11;
return createMolecule(1,atomPtr,anglePtr,bondPtr,dihedPtr,hopPtr,8,6,7,5,11);
}
vector<Molecule> createT3pdimMolecules(Opls_Scan *scanner)
{
// TIP3P Water Dimer Tot. E = -6.5396
//1 O 111 111 0 .000000 0 .000000 0 .000000 0
Atom atom1 = scanner->getAtom("111");
atom1.id=1;
//2 DU -1 -1 1 1.000000 0 .000000 0 .000000 0
Atom atom2=createAtom(2,-1,-1,-1,-1,-1,-1,NULL);
Bond bond2=createBond(2,1,1.0,false);
//3 DU -1 -1 2 1.000000 1 90.000000 0 .000000 0
Atom atom3=createAtom(3,-1,-1,-1,-1,-1,-1,NULL);
Bond bond3=createBond(3,2,1.0,false);
Angle angle3=createAngle(3,1,90.0,false);
//4 HO 112 112 1 .957200 2 127.740000 3 90.000000 0
Atom atom4=scanner->getAtom("112");
atom4.id=4;
Bond bond4=createBond(4,1,.957200,false);
Angle angle4=createAngle(4,2,127.740000,false);
Dihedral dihed4=createDihedral(4,3,90.00,false);
//5 HO 112 112 1 .957200 4 104.520000 2 180.000000 0
Atom atom5=scanner->getAtom("112");
atom5.id=5;
Bond bond5=createBond(5,1,.957200,false);
Angle angle5=createAngle(5,4,104.520000,false);
Dihedral dihed5=createDihedral(5,2,180.00,false);
//6 X -1 -1 1 .150000 4 52.260000 5 .000000 0
Atom atom6=createAtom(6,-1,-1,-1,-1,-1,-1,NULL);
Bond bond6=createBond(6,1,.150000,false);
Angle angle6=createAngle(6,4,52.260000,false);
Dihedral dihed6=createDihedral(6,5,.00,false);
//TERZ 2nd Bonded Molecule
//7 O 111 111 1 2.751259 2 131.716186 3 269.946364 0
Atom atom7=scanner->getAtom("111");
atom7.id=7;
Bond bond7=createBond(7,1,2.751259,false);
Angle angle7=createAngle(7,2,131.716186,false);
Dihedral dihed7=createDihedral(7,3,269.946364,false);
//8 DU -1 -1 7 1.000000 1 21.472391 2 179.887530 0
Atom atom8=createAtom(8,-1,-1,-1,-1,-1,-1,NULL);
Bond bond8=createBond(8,7,1.0,false);
Angle angle8=createAngle(8,1,21.472391,false);
Dihedral dihed8=createDihedral(8,2,179.887530,false);
//9 DU -1 -1 8 1.000000 7 90.000000 1 179.624613 0
Atom atom9=createAtom(9,-1,-1,-1,-1,-1,-1,NULL);
Bond bond9=createBond(9,8,1.0,false);
Angle angle9=createAngle(9,7,90.000000,false);
Dihedral dihed9=createDihedral(9,1,179.624613,false);
//10 HO 112 112 7 .957200 8 127.740000 9 90.000000 0
Atom atom10=scanner->getAtom("112");
atom10.id=10;
Bond bond10=createBond(10,7,0.957200,false);
Angle angle10=createAngle(10,8,127.74,false);
Dihedral dihed10=createDihedral(10,9,90.0,false);
//11 HO 112 112 7 .957200 10 104.520000 8 180.000000 0
Atom atom11=scanner->getAtom("112");
atom11.id=11;
Bond bond11=createBond(11,7,0.957200,false);
Angle angle11=createAngle(11,10,104.52,false);
Dihedral dihed11=createDihedral(11,8,180.0,false);
//12 X -1 -1 7 .150000 10 52.260000 11 .000000 0
Atom atom12=createAtom(12,-1,-1,-1,-1,-1,-1,NULL);
Bond bond12=createBond(12,7,0.15,false);
Angle angle12=createAngle(12,10,52.26,false);
Dihedral dihed12=createDihedral(12,11,0.0,false);
/* HOPS and BONDS Diagram of Mesh.z
//
//
// 10 11 12
// \ | /
// \|/
// 7--8--9
// |
// |
// 1--2--3
// /|\
// / | \
// 4 5 6
*/
//All intermolecular hops that have a hop distance >= 3
//bottom Molecule
Hop hop1=createHop(3,4,3);
Hop hop2=createHop(3,5,3);
Hop hop3=createHop(3,6,3);
//top Molecule
Hop hop4=createHop(9,10,3);
Hop hop5=createHop(9,11,3);
Hop hop6=createHop(9,12,3);
Atom *atomPtr = new Atom[6];
Bond *bondPtr = new Bond[5];
Angle *anglePtr = new Angle[4];
Dihedral *dihedPtr = new Dihedral[3];
Hop *hopPtr = new Hop[3];
vector<Molecule> retVect;
atomPtr[0]=atom1; atomPtr[1]=atom2; atomPtr[2]=atom3; atomPtr[3]=atom4; atomPtr[4]=atom5; atomPtr[5]=atom6;
bondPtr[0]=bond2; bondPtr[1]=bond3; bondPtr[2]=bond4; bondPtr[3]=bond5; bondPtr[4]=bond6;
anglePtr[0]=angle3; anglePtr[1]=angle4; anglePtr[2]=angle5; anglePtr[3]=angle6;
dihedPtr[0]=dihed4; dihedPtr[1]=dihed5; dihedPtr[2]=dihed6;
hopPtr[0]=hop1; hopPtr[1]=hop2; hopPtr[2]=hop3;
retVect.push_back( createMolecule(1,atomPtr,anglePtr,bondPtr,dihedPtr,hopPtr,6,4,5,3,3) );
Atom *atomPt = new Atom[6];
Bond *bondPt = new Bond[6];
Angle *anglePt = new Angle[6];
Dihedral *dihedPt = new Dihedral[6];
Hop *hopPt = new Hop[3];
atomPt[0]=atom7; atomPt[1]=atom8; atomPt[2]=atom9; atomPt[3]=atom10; atomPt[4]=atom11; atomPt[5]=atom12;
bondPt[0]=bond7; bondPt[1]=bond8; bondPt[2]=bond9; bondPt[3]=bond10; bondPt[4]=bond11; bondPt[5]=bond12;
anglePt[0]=angle7; anglePt[1]=angle8; anglePt[2]=angle9; anglePt[3]=angle10; anglePt[4]=angle11; anglePt[5]=angle12;
dihedPt[0]=dihed7; dihedPt[1]=dihed8; dihedPt[2]=dihed9; dihedPt[3]=dihed10; dihedPt[4]=dihed11; dihedPt[5]=dihed12;
hopPt[0]=hop4; hopPt[1]=hop5; hopPt[2]=hop6;
retVect.push_back( createMolecule(7,atomPt,anglePt,bondPt,dihedPt,hopPt,6,6,6,6,3) );
return retVect;
}
