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Improve the efficiency of regrowth move for branched molecules. In br…
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…anching point, we keep the configuration of all the branches, except one, to rebuild it using CBMC algorithm
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@msoroush
msoroush committed Sep 27, 2019
1 parent 72165bc commit e434b28
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Showing 4 changed files with 80 additions and 83 deletions.
83 changes: 41 additions & 42 deletions src/cbmc/DCCyclic.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -399,19 +399,18 @@ void DCCyclic::Regrowth(TrialMol& oldMol, TrialMol& newMol, uint molIndex)
newMol.AddAtom(partner, oldMol.AtomPosition(partner));
oldMol.ConfirmOldAtom(partner);
}

if(nodes[current].edges.size() == 1) {
//If current is the terminal node, continue building all edges
BuildEdges(oldMol, newMol, molIndex, current);
} else {
//First we pick a edge and continue copying the coordinate
//Then continue to build the rest of the molecule from current
//Copy the edges of the node to fringe
fringe = nodes[current].edges;
//First we pick a edge that will be fix and continue copy the coordinate
//We continue the same until only one edge left from this node
//If current is the terminal node, we dont enter to while loop
//Then continue to build the rest of the molecule from current

//Copy the edges of the node to currFringe
currFringe = nodes[current].edges;
while (currFringe.size() > 1) {
//randomely pick one one of the edges connected to fixNode
uint pickFixEdg = data.prng.randIntExc(fringe.size());
uint pickFixEdg = data.prng.randIntExc(currFringe.size());
//Travel to picked edges and make it as new fixNode
uint fixNode = fringe[pickFixEdg].destination;
uint fixNode = currFringe[pickFixEdg].destination;
visited[fixNode] = true;
destVisited[nodes[fixNode].atomIndex] = true;
//Copy the all atoms bonded to fixNode's focus
Expand Down Expand Up @@ -440,7 +439,7 @@ void DCCyclic::Regrowth(TrialMol& oldMol, TrialMol& newMol, uint molIndex)
newMol.AddAtom(partner, oldMol.AtomPosition(partner));
oldMol.ConfirmOldAtom(partner);
}
//Travel to new fixNode, remove traversed edge
//Travel to new fixNode, remove traverled edge
fringe[0] = fringe.back();
fringe.pop_back();
visited[fixNode] = true;
Expand All @@ -453,38 +452,38 @@ void DCCyclic::Regrowth(TrialMol& oldMol, TrialMol& newMol, uint molIndex)
}
}
}
//Now Start building the rest of the molecule from current
//Copy the edges of the current node to fringe
fringe = nodes[current].edges;
//Remove the fixed edge from fringe
fringe.erase(fringe.begin() + pickFixEdg);
for(uint i = 0; i < fringe.size(); i++) {
destVisited[fringe[i].atomIndex] = true;
}
//Advance along edges, building as we go
while(!fringe.empty()) {
//Randomely pick one of the edges connected to node
uint pick = data.prng.randIntExc(fringe.size());
DCComponent* comp = fringe[pick].connect;
//Call DCLinkedHedron and build all Atoms connected to selected edge
comp->PrepareNew(newMol, molIndex);
comp->BuildNew(newMol, molIndex);
comp->PrepareOld(oldMol, molIndex);
comp->BuildOld(oldMol, molIndex);
current = fringe[pick].destination;
//Remove the edge that we visited
fringe[pick] = fringe.back();
fringe.pop_back();
visited[current] = true;
for(uint i = 0; i < nodes[current].edges.size(); ++i) {
Edge& e = nodes[current].edges[i];
if(!visited[e.destination] && !destVisited[e.atomIndex]) {
fringe.push_back(e);
destVisited[e.atomIndex] = true;
}
//Remove the fixed edge from currFring
currFringe.erase(currFringe.begin() + pickFixEdg);
}

for(uint i = 0; i < currFringe.size(); i++) {
destVisited[currFringe[i].atomIndex] = true;
}
//Now Start building the rest of the molecule from current
//Start with only one left edge
//Advance along edges, building as we go
while(!currFringe.empty()) {
//Randomely pick one of the edges connected to node
uint pick = data.prng.randIntExc(currFringe.size());
DCComponent* comp = currFringe[pick].connect;
//Call DCLinkedCycle and build all Atoms connected to selected edge
comp->PrepareNew(newMol, molIndex);
comp->BuildNew(newMol, molIndex);
comp->PrepareOld(oldMol, molIndex);
comp->BuildOld(oldMol, molIndex);
current = currFringe[pick].destination;
//Remove the edge that we visited
currFringe[pick] = currFringe.back();
currFringe.pop_back();
visited[current] = true;
for(uint i = 0; i < nodes[current].edges.size(); ++i) {
Edge& e = nodes[current].edges[i];
if(!visited[e.destination] && !destVisited[e.atomIndex]) {
currFringe.push_back(e);
destVisited[e.atomIndex] = true;
}
}
}
}
}
}

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2 changes: 1 addition & 1 deletion src/cbmc/DCCyclic.h
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Original file line number Diff line number Diff line change
Expand Up @@ -79,7 +79,7 @@ class DCCyclic : public CBMC
std::vector<bool> isRing; //To check if atom is belong to a ring
std::vector<uint> ringIdx; //index to the row of cyclicAtoms
std::vector<Node> nodes;
std::vector<Edge> fringe;
std::vector<Edge> fringe, currFringe;
std::vector<bool> visited, destVisited;
std::vector<DCComponent*> crankshaft;
std::vector< std::vector<int> > cyclicAtoms;
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76 changes: 37 additions & 39 deletions src/cbmc/DCGraph.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -272,19 +272,18 @@ void DCGraph::Regrowth(TrialMol& oldMol, TrialMol& newMol, uint molIndex)
newMol.AddAtom(partner, oldMol.AtomPosition(partner));
oldMol.ConfirmOldAtom(partner);
}

if(nodes[current].edges.size() == 1) {
//If current is the terminal node, continue building all edges
BuildEdges(oldMol, newMol, molIndex, current);
} else {
//First we pick a edge and continue copying the coordinate
//Then continue to build the rest of the molecule from current
//Copy the edges of the node to fringe
fringe = nodes[current].edges;
//randomely pick one one of the edges connected to fixNode
uint pickFixEdg = data.prng.randIntExc(fringe.size());
//First we pick a edge that will be fix and continue copy the coordinate
//We continue the same until only one edge left from this node
//If current is the terminal node, we dont enter to while loop
//Then continue to build the rest of the molecule from current

//Copy the edges of the node to currFringe
currFringe = nodes[current].edges;
while (currFringe.size() > 1) {
//randomely pick one of the edges connected to current (fixNode)
uint pickFixEdg = data.prng.randIntExc(currFringe.size());
//Travel to picked edges and make it as new fixNode
uint fixNode = fringe[pickFixEdg].destination;
uint fixNode = currFringe[pickFixEdg].destination;
visited[fixNode] = true;
//Copy the all atoms bonded to fixNode's focus
for(uint b = 0; b < nodes[fixNode].partnerIndex.size(); b++) {
Expand All @@ -294,7 +293,7 @@ void DCGraph::Regrowth(TrialMol& oldMol, TrialMol& newMol, uint molIndex)
}
//Copy the edges of the new node to fringe
fringe = nodes[fixNode].edges;
//remove the edge that we travelled from
//remove the edge that we traveled from
for( uint f = 0; f < fringe.size(); f++) {
if(fringe[f].destination == current)
fringe.erase(fringe.begin() + f);
Expand All @@ -320,34 +319,33 @@ void DCGraph::Regrowth(TrialMol& oldMol, TrialMol& newMol, uint molIndex)
}
}
}
//Now Start building the rest of the molecule from current
//Copy the edges of the current node to fringe
fringe = nodes[current].edges;
//Remove the fixed edge from fringe
fringe.erase(fringe.begin() + pickFixEdg);
//Advance along edges, building as we go
while(!fringe.empty()) {
//Randomely pick one of the edges connected to node
uint pick = data.prng.randIntExc(fringe.size());
DCComponent* comp = fringe[pick].component;
//Call DCLinkedHedron and build all Atoms connected to selected edge
comp->PrepareNew(newMol, molIndex);
comp->BuildNew(newMol, molIndex);
comp->PrepareOld(oldMol, molIndex);
comp->BuildOld(oldMol, molIndex);
current = fringe[pick].destination;
//Remove the edge that we visited
fringe[pick] = fringe.back();
fringe.pop_back();
visited[current] = true;
for(uint i = 0; i < nodes[current].edges.size(); ++i) {
Edge& e = nodes[current].edges[i];
if(!visited[e.destination]) {
fringe.push_back(e);
}
//Remove the fixed edge from currFring
currFringe.erase(currFringe.begin() + pickFixEdg);
}
//Now Start building the rest of the molecule from current
//Start with only one left edge
//Advance along edges, building as we go
while(!currFringe.empty()) {
//Randomely pick one of the edges connected to node
uint pick = data.prng.randIntExc(currFringe.size());
DCComponent* comp = currFringe[pick].component;
//Call DCLinkedHedron and build all Atoms connected to selected edge
comp->PrepareNew(newMol, molIndex);
comp->BuildNew(newMol, molIndex);
comp->PrepareOld(oldMol, molIndex);
comp->BuildOld(oldMol, molIndex);
current = currFringe[pick].destination;
//Remove the edge that we visited
currFringe[pick] = currFringe.back();
currFringe.pop_back();
visited[current] = true;
for(uint i = 0; i < nodes[current].edges.size(); ++i) {
Edge& e = nodes[current].edges[i];
if(!visited[e.destination]) {
currFringe.push_back(e);
}
}
}
}
}
}

Expand Down
2 changes: 1 addition & 1 deletion src/cbmc/DCGraph.h
View file
Original file line number Diff line number Diff line change
Expand Up @@ -74,7 +74,7 @@ class DCGraph : public CBMC
DCData data;
bool hasCrankShaft;
std::vector<Node> nodes;
std::vector<Edge> fringe;
std::vector<Edge> fringe, currFringe;
std::vector<bool> visited;
std::vector<DCComponent*> shaftNodes;
XYZArray coords;
Expand Down

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