int Traj_AmberNetcdf::parallelReadFrame(int set, Frame& frameIn) {
MPI_Offset pstart_[3];
MPI_Offset pcount_[3];
pstart_[0] = set;
pstart_[1] = 0;
pstart_[2] = 0;
pcount_[0] = 1;
pcount_[1] = Ncatom();
pcount_[2] = 3;
//int err = ncmpi_get_vara_float_all(ncid_, coordVID_, pstart_, pcount_, Coord_);
int err = ncmpi_get_vara_float(ncid_, coordVID_, pstart_, pcount_, Coord_);
if (checkPNCerr(err)) return Parallel::Abort(err);
FloatToDouble(frameIn.xAddress(), Coord_);
if (velocityVID_ != -1) {
//err = ncmpi_get_vara_float_all(ncid_, velocityVID_, pstart_, pcount_, Coord_);
err = ncmpi_get_vara_float(ncid_, velocityVID_, pstart_, pcount_, Coord_);
if (checkPNCerr(err)) return Parallel::Abort(err);
FloatToDouble(frameIn.vAddress(), Coord_);
}
if (frcVID_ != -1) {
err = ncmpi_get_vara_float(ncid_, frcVID_, pstart_, pcount_, Coord_);
if (checkPNCerr(err)) return Parallel::Abort(err);
FloatToDouble(frameIn.fAddress(), Coord_);
}
pcount_[2] = 0;
if (cellLengthVID_ != -1) {
pcount_[1] = 3;
//err = ncmpi_get_vara_double_all(ncid_, cellLengthVID_, pstart_, pcount_, frameIn.bAddress());
err = ncmpi_get_vara_double(ncid_, cellLengthVID_, pstart_, pcount_, frameIn.bAddress());
if (checkPNCerr(err)) return Parallel::Abort(err);
//err = ncmpi_get_vara_double_all(ncid_, cellAngleVID_, pstart_, pcount_, frameIn.bAddress()+3);
err = ncmpi_get_vara_double(ncid_, cellAngleVID_, pstart_, pcount_, frameIn.bAddress()+3);
}
if (TempVID_ != -1) {
//err = ncmpi_get_vara_double_all(ncid_, TempVID_, pstart_, pcount_, frameIn.tAddress());
err = ncmpi_get_vara_double(ncid_, TempVID_, pstart_, pcount_, frameIn.tAddress());
if (checkPNCerr(err)) return Parallel::Abort(err);
}
if (timeVID_ != -1) {
float time;
err = ncmpi_get_vara_float(ncid_, timeVID_, pstart_, pcount_, &time);
if (checkPNCerr(err)) return Parallel::Abort(err);
frameIn.SetTime( (double)time );
}
if (indicesVID_ != -1) {
pcount_[1] = remd_dimension_;
//err = ncmpi_get_vara_int_all(ncid_, indicesVID_, pstart_, pcount_, frameIn.iAddress());
err = ncmpi_get_vara_int(ncid_, indicesVID_, pstart_, pcount_, frameIn.iAddress());
if (checkPNCerr(err)) return Parallel::Abort(err);
}
return 0;
}
/** Get the specified frame from amber netcdf file
* Coords are a 1 dimensional array of format X1,Y1,Z1,X2,Y2,Z2,...
*/
int Traj_AmberNetcdf::readFrame(int set,double *X, double *V,double *box, double *T) {
// Get temperature
if (TempVID_!=-1) {
start_[0] = set;
count_[0] = 1;
if ( checkNCerr(nc_get_vara_double(ncid_, TempVID_, start_, count_, T)) ) {
mprinterr("Error: Getting replica temperature.\n");
return 1;
}
//fprintf(stderr,"DEBUG: Replica Temperature %lf\n",F->T);
}
// Read Coords
start_[0] = set;
start_[1] = 0;
start_[2] = 0;
count_[0] = 1;
count_[1] = Ncatom();
count_[2] = 3;
if ( checkNCerr(nc_get_vara_float(ncid_, coordVID_, start_, count_, Coord_)) ) {
mprinterr("Error: Getting frame %i\n", set);
return 1;
}
FloatToDouble(X, Coord_);
// Read Velocities
if (velocityVID_ != -1) {
if ( checkNCerr(nc_get_vara_float(ncid_, velocityVID_, start_, count_, Veloc_)) ) {
mprinterr("Error: Getting velocities for frame %i\n", set);
return 1;
}
FloatToDouble(V, Veloc_);
}
// Read box info
if (cellLengthVID_ != -1) {
count_[1] = 3;
count_[2] = 0;
if ( checkNCerr(nc_get_vara_double(ncid_, cellLengthVID_, start_, count_, box)) ) {
mprinterr("Getting cell lengths.\n");
return 1;
}
if ( checkNCerr(nc_get_vara_double(ncid_, cellAngleVID_, start_, count_, box+3)) ) {
mprinterr("Getting cell angles.\n");
return 1;
}
}
return 0;
}
JNIEXPORT jint JNICALL Java_edu_berkeley_bid_CUMATD_FloatToDouble
(JNIEnv *env, jobject obj, jobject jA, jobject jB, jint N)
{
float *A = (float*)getPointer(env, jA);
double *B = (double*)getPointer(env, jB);
return FloatToDouble(A, B, N);
}
// As DeSerialize, but reads an old (float) format WeightMatrix for
// backward compatibility.
bool WeightMatrix::DeSerializeOld(bool training, bool swap, TFile* fp) {
GENERIC_2D_ARRAY<float> float_array;
if (int_mode_) {
if (!wi_.DeSerialize(swap, fp)) return false;
GenericVector<float> old_scales;
if (!old_scales.DeSerialize(swap, fp)) return false;
scales_.init_to_size(old_scales.size(), 0.0);
for (int i = 0; i < old_scales.size(); ++i) scales_[i] = old_scales[i];
} else {
if (!float_array.DeSerialize(swap, fp)) return false;
FloatToDouble(float_array, &wf_);
}
if (training) {
InitBackward(use_ada_grad_);
if (!float_array.DeSerialize(swap, fp)) return false;
FloatToDouble(float_array, &updates_);
// Errs was only used in int training, which is now dead.
if (!float_array.DeSerialize(swap, fp)) return false;
}
return true;
}
// Traj_AmberNetcdf::readVelocity()
int Traj_AmberNetcdf::readVelocity(int set, Frame& frameIn) {
start_[0] = set;
start_[1] = 0;
start_[2] = 0;
count_[0] = 1;
count_[1] = Ncatom();
count_[2] = 3;
// Read Velocities
if (velocityVID_ != -1) {
if ( checkNCerr(nc_get_vara_float(ncid_, velocityVID_, start_, count_, Coord_)) ) {
mprinterr("Error: Getting velocities for frame %i\n", set+1);
return 1;
}
FloatToDouble(frameIn.vAddress(), Coord_);
}
return 0;
}
// Traj_AmberNetcdf::readForce()
int Traj_AmberNetcdf::readForce(int set, Frame& frameIn) {
start_[0] = set;
start_[1] = 0;
start_[2] = 0;
count_[0] = 1;
count_[1] = Ncatom();
count_[2] = 3;
// Read forces
if (frcVID_ != -1) {
if ( NC::CheckErr(nc_get_vara_float(ncid_, frcVID_, start_, count_, Coord_)) ) {
mprinterr("Error: Getting forces for frame %i\n", set+1);
return 1;
}
FloatToDouble(frameIn.fAddress(), Coord_);
}
return 0;
}
TEST(DSP, FloatDoubleConversion)
{
float in[10] = {1.0, -1.0, 1.0, -1.0, 1.0, -1.0, 1.0, -1.0, 1.0, -1.0};
double out[10];
float fout[10];
FloatToDouble(out, in, 10);
for (unsigned i = 0; i < 10; ++i)
{
ASSERT_DOUBLE_EQ((double)in[i], out[i]);
}
DoubleToFloat(fout, out, 10);
for (unsigned i = 0; i < 10; ++i)
{
ASSERT_FLOAT_EQ(in[i], fout[i]);
}
}
// Traj_NcEnsemble::readArray() //TODO RemdValues
int Traj_NcEnsemble::readArray(int set, FrameArray& f_ensemble) {
# ifdef HAS_PNETCDF
MPI_Offset pstart_[4];
MPI_Offset pcount_[4];
# define start_ pstart_
# define count_ pcount_
# endif
start_[0] = set; // Frame
start_[2] = 0; // Atoms
start_[3] = 0; // XYZ
count_[0] = 1; // Frame
count_[1] = 1; // Ensemble
count_[3] = 3; // XYZ
//rprintf("DEBUG: Reading frame %i\n", set+1);
for (int member = ensembleStart_; member != ensembleEnd_; member++) {
# ifdef MPI
Frame& frm = f_ensemble[0];
# else
Frame& frm = f_ensemble[member];
# endif
start_[1] = member; // Ensemble
count_[2] = Ncatom(); // Atoms
// Read Coords
# ifdef HAS_PNETCDF
if (checkPNCerr(ncmpi_get_vara_float_all(ncid_, coordVID_, start_, count_, Coord_)))
# else
if (NC::CheckErr(nc_get_vara_float(ncid_, coordVID_, start_, count_, Coord_)))
# endif
{
rprinterr("Error: Getting coordinates for frame %i\n", set+1);
return 1;
}
FloatToDouble(frm.xAddress(), Coord_);
//mprintf("Frm=%8i Rep=%8i ", set+1, member+1); // DEBUG
//frm.printAtomCoord(0); // DEBUG
// Read Velocities
if (velocityVID_ != -1) {
# ifdef HAS_PNETCDF
if (checkPNCerr(ncmpi_get_vara_float_all(ncid_, velocityVID_, start_, count_, Coord_)))
# else
if (NC::CheckErr(nc_get_vara_float(ncid_, velocityVID_, start_, count_, Coord_)))
# endif
{
rprinterr("Error: Getting velocities for frame %i\n", set+1);
return 1;
}
FloatToDouble(frm.vAddress(), Coord_);
}
// Read Box
if (cellLengthVID_ != -1) {
count_[2] = 3;
# ifdef HAS_PNETCDF
if (checkPNCerr(ncmpi_get_vara_double_all(ncid_, cellLengthVID_, start_, count_, frm.bAddress())))
# else
if (NC::CheckErr(nc_get_vara_double(ncid_, cellLengthVID_, start_, count_, frm.bAddress())))
# endif
{
rprinterr("Error: Getting cell lengths for frame %i.\n", set+1);
return 1;
}
# ifdef HAS_PNETCDF
if (checkPNCerr(ncmpi_get_vara_double_all(ncid_, cellAngleVID_, start_, count_, frm.bAddress()+3)))
# else
if (NC::CheckErr(nc_get_vara_double(ncid_, cellAngleVID_, start_, count_, frm.bAddress()+3)))
# endif
{
rprinterr("Error: Getting cell angles for frame %i.\n", set+1);
return 1;
}
}
// Read Temperature
if (TempVID_!=-1) {
# ifdef HAS_PNETCDF
if (checkPNCerr(ncmpi_get_vara_double_all(ncid_, TempVID_, start_, count_, frm.tAddress())))
# else
if (NC::CheckErr(nc_get_vara_double(ncid_, TempVID_, start_, count_, frm.tAddress())))
# endif
{
rprinterr("Error: Getting replica temperature for frame %i.\n", set+1);
return 1;
}
//fprintf(stderr,"DEBUG: Replica Temperature %lf\n",F->T);
}
// Read indices
if (indicesVID_!=-1) {
count_[2] = remd_dimension_;
# ifdef HAS_PNETCDF
if (checkPNCerr(ncmpi_get_vara_int_all(ncid_, indicesVID_, start_, count_, frm.iAddress())))
# else
if (NC::CheckErr(nc_get_vara_int(ncid_, indicesVID_, start_, count_, frm.iAddress())))
# endif
{
rprinterr("Error: Getting replica indices for frame %i.\n", set+1);
return 1;
}
// DEBUG
//char buffer[128];
//char* ptr = buffer;
//ptr += sprintf(buffer,"DEBUG:\tReplica indices:");
//for (int dim=0; dim < remd_dimension_; dim++) ptr += sprintf(ptr, " %i", frm.RemdIndices()[dim]);
//sprintf(ptr,"\n");
//rprintf("%s", buffer);
}
}
# ifdef HAS_PNETCDF
// DEBUG
# undef start_
# undef count_
# endif
return 0;
}
/** Get the specified frame from amber netcdf file
* Coords are a 1 dimensional array of format X1,Y1,Z1,X2,Y2,Z2,...
*/
int Traj_AmberNetcdf::readFrame(int set, Frame& frameIn) {
start_[0] = set;
start_[1] = 0;
start_[2] = 0;
count_[0] = 1;
count_[1] = Ncatom();
count_[2] = 3;
// Get temperature
if (TempVID_!=-1) {
if ( checkNCerr(nc_get_vara_double(ncid_, TempVID_, start_, count_, frameIn.tAddress())) ) {
mprinterr("Error: Getting replica temperature for frame %i.\n", set+1);
return 1;
}
//fprintf(stderr,"DEBUG: Replica Temperature %lf\n",F->T);
}
// Get time
if (timeVID_!=-1) {
float time;
if (checkNCerr(nc_get_vara_float(ncid_, timeVID_, start_, count_, &time))) {
mprinterr("Error: Getting time for frame %i.\n", set + 1);
return 1;
}
frameIn.SetTime( (double)time );
}
// Read Coords
if ( checkNCerr(nc_get_vara_float(ncid_, coordVID_, start_, count_, Coord_)) ) {
mprinterr("Error: Getting coordinates for frame %i\n", set+1);
return 1;
}
FloatToDouble(frameIn.xAddress(), Coord_);
// Read Velocities
if (velocityVID_ != -1) {
if ( checkNCerr(nc_get_vara_float(ncid_, velocityVID_, start_, count_, Coord_)) ) {
mprinterr("Error: Getting velocities for frame %i\n", set+1);
return 1;
}
FloatToDouble(frameIn.vAddress(), Coord_);
}
// Read indices. Input array must be allocated to be size remd_dimension.
if (indicesVID_!=-1) {
count_[1] = remd_dimension_;
if ( checkNCerr(nc_get_vara_int(ncid_, indicesVID_, start_, count_, frameIn.iAddress())) ) {
mprinterr("Error: Getting replica indices for frame %i.\n", set+1);
return 1;
}
//mprintf("DEBUG:\tReplica indices:");
//for (int dim=0; dim < remd_dimension_; dim++) mprintf(" %i",remd_indices[dim]);
//mprintf("\n");
}
// Read box info
if (cellLengthVID_ != -1) {
count_[1] = 3;
count_[2] = 0;
if (checkNCerr(nc_get_vara_double(ncid_, cellLengthVID_, start_, count_, frameIn.bAddress())))
{
mprinterr("Error: Getting cell lengths for frame %i.\n", set+1);
return 1;
}
if (checkNCerr(nc_get_vara_double(ncid_, cellAngleVID_, start_, count_, frameIn.bAddress()+3)))
{
mprinterr("Error: Getting cell angles for frame %i.\n", set+1);
return 1;
}
}
return 0;
}