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Added ability to cache DCD frames in DCD writer, currently set to 1 f…
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…rame. Requires parameter to pass through from OutputDCD.
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@chrissweet
chrissweet committed Dec 4, 2014
1 parent fe3b762 commit 205896f
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Showing 2 changed files with 100 additions and 43 deletions.
135 changes: 93 additions & 42 deletions protomol/io/DCDTrajectoryWriter.cpp
View file
Original file line number Diff line number Diff line change
Expand Up @@ -15,29 +15,38 @@ DCDTrajectoryWriter::DCDTrajectoryWriter(Real timestep, unsigned int firststep,
Writer(ios::binary | ios::trunc), myFrameOffset(0),
myIsLittleEndian(isLittleEndian),
myFirstStep(firststep), myTimeStep(timestep),
firstWrite(true) {}
firstWrite(true), cachesize(1), firstFlushOffset(1) {
}

DCDTrajectoryWriter::DCDTrajectoryWriter(const string &filename, Real timestep,
unsigned int firststep,
bool isLittleEndian) :
Writer(ios::binary | ios::trunc, filename), myFrameOffset(0),
myIsLittleEndian(isLittleEndian), myFirstStep(firststep),
myTimeStep(timestep), firstWrite(true) {}
myTimeStep(timestep), firstWrite(true), cachesize(1), firstFlushOffset(1) {
}

DCDTrajectoryWriter::DCDTrajectoryWriter(std::ios::openmode mode, int frameoffs,
const string &filename, Real timestep,
unsigned int firststep,
bool isLittleEndian) :
Writer(mode, filename), myFrameOffset(frameoffs),
myIsLittleEndian(isLittleEndian), myFirstStep(firststep),
myTimeStep(timestep), firstWrite(true) {}
myTimeStep(timestep), firstWrite(true), cachesize(1), firstFlushOffset(1) {
}

DCDTrajectoryWriter::DCDTrajectoryWriter(const char *filename, Real timestep,
unsigned int firststep,
bool isLittleEndian) :
Writer(ios::binary | ios::trunc, string(filename)), myFrameOffset(0),
myIsLittleEndian(isLittleEndian), myFirstStep(firststep),
myTimeStep(timestep), firstWrite(true) {}
myTimeStep(timestep), firstWrite(true), cachesize(1), firstFlushOffset(1) {
}

DCDTrajectoryWriter::~DCDTrajectoryWriter(){
Vector3DBlock zerolength;
write(zerolength);
}

bool DCDTrajectoryWriter::openWith(Real timestep, unsigned int firststep,
bool isLittleEndian) {
Expand Down Expand Up @@ -65,7 +74,7 @@ bool DCDTrajectoryWriter::openWith(const char *filename, Real timestep,
return open(filename);
}

bool DCDTrajectoryWriter::reopen(unsigned int numAtoms) {
bool DCDTrajectoryWriter::reopen(unsigned int numAtoms, unsigned int numberOfSets) {
if (!is_open()) {
open(filename, ios::binary | ios::in | ios::out);
if (!is_open()) THROWS("Failed to open '" << filename << "'");
Expand Down Expand Up @@ -121,11 +130,14 @@ bool DCDTrajectoryWriter::reopen(unsigned int numAtoms) {
THROWS("Corrupt DCD file. Size is " << size << ", should be >= " << calculateSize << ".");

//correct numsets
numSets = ++myFrameOffset;
myFrameOffset += numberOfSets;
numSets = myFrameOffset;
//was numSets = ++myFrameOffset, but now save multiple steps;

}else{
//original code here
++numSets;
numSets += numberOfSets;
//++numSets;
}

//back to original code
Expand All @@ -147,7 +159,7 @@ bool DCDTrajectoryWriter::reopen(unsigned int numAtoms) {
file.seekg(0, ios::beg);

int32 nAtoms = static_cast<int32>(numAtoms);
int32 numSets = 1;
int32 numSets = numberOfSets; //was 1, now set to number we are writing;
int32 numSteps = 1;
int32 firstStep = static_cast<int32>(myFirstStep);
float4 timeStep =
Expand Down Expand Up @@ -236,42 +248,81 @@ bool DCDTrajectoryWriter::write(const Vector3DBlock &coords) {
return true;
}

//original code
const unsigned int count = coords.size();
if (!reopen(count)) return false;

myX.resize(count);
myY.resize(count);
myZ.resize(count);
//added caching to lower IO calls
if( coords.size() != 0 ) cachedCoords.push_back(coords);

//disable forward save if cachesize is 1)
if( cachesize == 1 ) firstFlushOffset = 0;

//push out if sufficient
if( cachedCoords.size() >= (cachesize + firstFlushOffset) || ( coords.size() == 0 && cachedCoords.size() > 0 )){
//report << debug(0) <<"Writing DCD." << endr;

//clear first flush offset so that output is synced with checkpoint
firstFlushOffset = 0;

//original code modified for caching, index 0 must exist here
const unsigned int setcount = cachedCoords.size();
const unsigned int count = cachedCoords[0].size();//ccoords.size();
if (!reopen(count, setcount)) return false;

//loop over each set of coordinates
for( int i=0; i<setcount; i++){
Vector3DBlock ccoords = cachedCoords[i];

//original code
//const unsigned int count = ccoords.size();
//if (!reopen(count)) return false;

myX.resize(count);
myY.resize(count);
myZ.resize(count);

for (unsigned int i = 0; i < count; ++i) {
myX[i] = static_cast<float>(ccoords[i].c[0]);
myY[i] = static_cast<float>(ccoords[i].c[1]);
myZ[i] = static_cast<float>(ccoords[i].c[2]);
if (myIsLittleEndian != ISLITTLEENDIAN) {
swapBytes(myX[i]);
swapBytes(myY[i]);
swapBytes(myZ[i]);
}
}

int32 nAtoms = static_cast<int32>(count * 4);
if (myIsLittleEndian != ISLITTLEENDIAN) swapBytes(nAtoms);

file.write((char *)&nAtoms, sizeof(int32));
file.write((char *)&(myX[0]), count * sizeof(float4));
file.write((char *)&nAtoms, sizeof(int32));

file.write((char *)&nAtoms, sizeof(int32));
file.write((char *)&(myY[0]), count * sizeof(float4));
file.write((char *)&nAtoms, sizeof(int32));

file.write((char *)&nAtoms, sizeof(int32));
file.write((char *)&(myZ[0]), count * sizeof(float4));
file.write((char *)&nAtoms, sizeof(int32));

//close();

if( file.fail() ){
cachedCoords.clear();
close();
return false;
}//end of coordinate save

}//end of loop

//close file once strored
close();
cachedCoords.clear();
return true;//!file.fail();

for (unsigned int i = 0; i < count; ++i) {
myX[i] = static_cast<float>(coords[i].c[0]);
myY[i] = static_cast<float>(coords[i].c[1]);
myZ[i] = static_cast<float>(coords[i].c[2]);
if (myIsLittleEndian != ISLITTLEENDIAN) {
swapBytes(myX[i]);
swapBytes(myY[i]);
swapBytes(myZ[i]);
}
}

int32 nAtoms = static_cast<int32>(count * 4);
if (myIsLittleEndian != ISLITTLEENDIAN) swapBytes(nAtoms);

file.write((char *)&nAtoms, sizeof(int32));
file.write((char *)&(myX[0]), count * sizeof(float4));
file.write((char *)&nAtoms, sizeof(int32));

file.write((char *)&nAtoms, sizeof(int32));
file.write((char *)&(myY[0]), count * sizeof(float4));
file.write((char *)&nAtoms, sizeof(int32));

file.write((char *)&nAtoms, sizeof(int32));
file.write((char *)&(myZ[0]), count * sizeof(float4));
file.write((char *)&nAtoms, sizeof(int32));

close();
return !file.fail();

//true if just cached
return true;
}

void DCDTrajectoryWriter::setLittleEndian(bool littleEndian) {
Expand Down
8 changes: 7 additions & 1 deletion protomol/io/DCDTrajectoryWriter.h
View file
Original file line number Diff line number Diff line change
Expand Up @@ -42,6 +42,7 @@ namespace ProtoMol {
Real timestep = 1.0, unsigned int firststep =
1,
bool isLittleEndian = ISLITTLEENDIAN);
virtual ~DCDTrajectoryWriter();

//special create for append to DCD
explicit DCDTrajectoryWriter(std::ios::openmode mode, int frameoffs,
Expand Down Expand Up @@ -71,7 +72,7 @@ namespace ProtoMol {
void setTimestep(Real timestep);
void setFirststep(unsigned int firststep);

bool reopen(unsigned int numAtoms);
bool reopen(unsigned int numAtoms, unsigned int numberOfSets);

//~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
// Friends
Expand All @@ -95,6 +96,11 @@ namespace ProtoMol {
std::vector<float4> myX;
std::vector<float4> myY;
std::vector<float4> myZ;

//additions to cache data
std::vector<Vector3DBlock> cachedCoords;
unsigned int cachesize;
unsigned int firstFlushOffset;
};

//____INLINES
Expand Down

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