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[WIP] Implement additional structure and force weights in the loss function #187

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[WIP] Implement additional structure and force weights in the loss function #187

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4 changes: 3 additions & 1 deletion src/libnnp/Atom.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -37,7 +37,8 @@ Atom::Atom() : hasNeighborList (false),
numSymmetryFunctions (0 ),
energy (0.0 ),
charge (0.0 ),
chargeRef (0.0 )
chargeRef (0.0 ),
forceWeight (1.0 )
{
}

Expand Down Expand Up @@ -363,6 +364,7 @@ vector<string> Atom::info() const
v.push_back(strpr("energy : %16.8E\n", energy));
v.push_back(strpr("charge : %16.8E\n", charge));
v.push_back(strpr("chargeRef : %16.8E\n", chargeRef));
v.push_back(strpr("forceWeight : %16.8E\n", forceWeight));
v.push_back(strpr("r : %16.8E %16.8E %16.8E\n", r[0], r[1], r[2]));
v.push_back(strpr("f : %16.8E %16.8E %16.8E\n", f[0], f[1], f[2]));
v.push_back(strpr("fRef : %16.8E %16.8E %16.8E\n", fRef[0], fRef[1], fRef[2]));
Expand Down
2 changes: 2 additions & 0 deletions src/libnnp/Atom.h
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Expand Up @@ -114,6 +114,8 @@ struct Atom
double charge;
/// Atomic reference charge.
double chargeRef;
/// Force weight for training.
double forceWeight;
/// Cartesian coordinates
Vec3D r;
/// Force vector calculated by neural network.
Expand Down
10 changes: 10 additions & 0 deletions src/libnnp/Structure.cpp
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Expand Up @@ -42,6 +42,7 @@ Structure::Structure() :
charge (0.0 ),
chargeRef (0.0 ),
volume (0.0 ),
strucWeight (1.0 ),
sampleType (ST_UNKNOWN),
comment ("" )
{
Expand Down Expand Up @@ -206,6 +207,10 @@ void Structure::readFromLines(vector<string> const& lines)
atoms.back().r[2] = atof(splitLine.at(3).c_str());
atoms.back().element = elementMap[splitLine.at(4)];
atoms.back().chargeRef = atof(splitLine.at(5).c_str());
atoms.back().forceWeight = atof(splitLine.at(6).c_str());
if (atoms.back().forceWeight == 0) {
atoms.back().forceWeight = 1.0;
}
atoms.back().fRef[0] = atof(splitLine.at(7).c_str());
atoms.back().fRef[1] = atof(splitLine.at(8).c_str());
atoms.back().fRef[2] = atof(splitLine.at(9).c_str());
Expand All @@ -221,6 +226,10 @@ void Structure::readFromLines(vector<string> const& lines)
{
chargeRef = atof(splitLine[1].c_str());
}
else if (splitLine.at(0) == "weight")
{
strucWeight = atof(splitLine[1].c_str());
}
else if (splitLine.at(0) == "end")
{
if (!(iBoxVector == 0 || iBoxVector == 3))
Expand Down Expand Up @@ -555,6 +564,7 @@ void Structure::reset()
charge = 0.0 ;
chargeRef = 0.0 ;
volume = 0.0 ;
strucWeight = 1.0 ;
sampleType = ST_UNKNOWN;
comment = "" ;

Expand Down
2 changes: 2 additions & 0 deletions src/libnnp/Structure.h
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Expand Up @@ -82,6 +82,8 @@ struct Structure
double chargeRef;
/// Simulation box volume.
double volume;
/// Structure weight
double strucWeight;
/// Sample type (training or test set).
SampleType sampleType;
/// Structure comment.
Expand Down
8 changes: 6 additions & 2 deletions src/libnnptrain/Dataset.cpp
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Expand Up @@ -179,7 +179,7 @@ int Dataset::calculateBufferSize(Structure const& structure) const
MPI_Pack_size(1, MPI_CHAR , comm, &cs );

// Structure
bs += 5 * cs + 4 * ss + 4 * is + 5 * ds;
bs += 5 * cs + 4 * ss + 4 * is + 6 * ds;
// Structure.comment
bs += ss;
bs += (s.comment.length() + 1) * cs;
Expand All @@ -192,7 +192,7 @@ int Dataset::calculateBufferSize(Structure const& structure) const
bs += s.numAtomsPerElement.size() * ss;
// Structure.atoms
bs += ss;
bs += s.atoms.size() * (4 * cs + 6 * ss + i64s + 3 * ds + 3 * 3 * ds);
bs += s.atoms.size() * (4 * cs + 6 * ss + i64s + 4 * ds + 3 * 3 * ds);
for (vector<Atom>::const_iterator it = s.atoms.begin();
it != s.atoms.end(); ++it)
{
Expand Down Expand Up @@ -275,6 +275,7 @@ int Dataset::sendStructure(Structure const& structure, int dest) const
MPI_Pack(&(s.charge ), 1, MPI_DOUBLE, buf, bs, &p, comm);
MPI_Pack(&(s.chargeRef ), 1, MPI_DOUBLE, buf, bs, &p, comm);
MPI_Pack(&(s.volume ), 1, MPI_DOUBLE, buf, bs, &p, comm);
MPI_Pack(&(s.strucWeight ), 1, MPI_DOUBLE, buf, bs, &p, comm);
MPI_Pack(&(s.sampleType ), 1, MPI_INT , buf, bs, &p, comm);

// Strucuture.comment
Expand Down Expand Up @@ -325,6 +326,7 @@ int Dataset::sendStructure(Structure const& structure, int dest) const
MPI_Pack(&(it->energy ), 1, MPI_DOUBLE , buf, bs, &p, comm);
MPI_Pack(&(it->charge ), 1, MPI_DOUBLE , buf, bs, &p, comm);
MPI_Pack(&(it->chargeRef ), 1, MPI_DOUBLE , buf, bs, &p, comm);
MPI_Pack(&(it->forceWeight ), 1, MPI_DOUBLE , buf, bs, &p, comm);
MPI_Pack(&(it->r.r ), 3, MPI_DOUBLE , buf, bs, &p, comm);
MPI_Pack(&(it->f.r ), 3, MPI_DOUBLE , buf, bs, &p, comm);
MPI_Pack(&(it->fRef.r ), 3, MPI_DOUBLE , buf, bs, &p, comm);
Expand Down Expand Up @@ -492,6 +494,7 @@ int Dataset::recvStructure(Structure* const structure, int src)
MPI_Unpack(buf, bs, &p, &(s->charge ), 1, MPI_DOUBLE, comm);
MPI_Unpack(buf, bs, &p, &(s->chargeRef ), 1, MPI_DOUBLE, comm);
MPI_Unpack(buf, bs, &p, &(s->volume ), 1, MPI_DOUBLE, comm);
MPI_Unpack(buf, bs, &p, &(s->strucWeight ), 1, MPI_DOUBLE, comm);
MPI_Unpack(buf, bs, &p, &(s->sampleType ), 1, MPI_INT , comm);

// Strucuture.comment
Expand Down Expand Up @@ -549,6 +552,7 @@ int Dataset::recvStructure(Structure* const structure, int src)
MPI_Unpack(buf, bs, &p, &(it->energy ), 1, MPI_DOUBLE , comm);
MPI_Unpack(buf, bs, &p, &(it->charge ), 1, MPI_DOUBLE , comm);
MPI_Unpack(buf, bs, &p, &(it->chargeRef ), 1, MPI_DOUBLE , comm);
MPI_Unpack(buf, bs, &p, &(it->forceWeight ), 1, MPI_DOUBLE , comm);
MPI_Unpack(buf, bs, &p, &(it->r.r ), 3, MPI_DOUBLE , comm);
MPI_Unpack(buf, bs, &p, &(it->f.r ), 3, MPI_DOUBLE , comm);
MPI_Unpack(buf, bs, &p, &(it->fRef.r ), 3, MPI_DOUBLE , comm);
Expand Down
4 changes: 2 additions & 2 deletions src/libnnptrain/Training.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -2451,12 +2451,12 @@ void Training::update(string const& property)
{
if (k == "energy")
{
pu.error.at(0).at(offset2) += s.energyRef - s.energy;
pu.error.at(0).at(offset2) += (s.energyRef - s.energy) * s.strucWeight;
}
else if (k == "force")
{
Atom const& a = s.atoms.at(c->a);
pu.error.at(0).at(offset2) += a.fRef[c->c] - a.f[c->c];
pu.error.at(0).at(offset2) += (a.fRef[c->c] - a.f[c->c]) * s.strucWeight * a.forceWeight;
}
else if (k == "charge")
{
Expand Down