diff --git a/bin/qp_convert_h5_to_ezfio b/bin/qp_convert_h5_to_ezfio index 5a397d3f..49e034b4 100755 --- a/bin/qp_convert_h5_to_ezfio +++ b/bin/qp_convert_h5_to_ezfio @@ -17,6 +17,7 @@ import sys import numpy as np import os from docopt import docopt +import gzip #fname = sys.argv[1] #qph5name = sys.argv[2] @@ -26,6 +27,93 @@ def get_full_path(file_path): # file_path = os.path.abspath(file_path) return file_path + +def flatten(l): + res = [] + for i in l: + if hasattr(i, "__iter__") and not isinstance(i, str): + res.extend(flatten(i)) + else: + res.append(i) + return res + +#def write_array_do(self,dir,fil,rank,dims,dim_max,dat): +# if self.read_only: +# self.error('Read-only file.') +# l_filename = [ tempfile.mktemp(dir=dir.strip()), dir.strip()+'/'+fil+'.gz' ] +# try: +# file = StringIO.StringIO() +# file.write("%3d\n"%(rank,)) +# for d in dims: +# file.write("%20d "%(d,)) +# file.write("\n") +# +# dat = flatten(dat) +# for i in range(dim_max): +# file.write("%24.15E\n"%(dat[i],)) +# file.flush() +# buffer = file.getvalue() +# file.close() +# file = GzipFile(filename=l_filename[0],mode='wb') +# file.write(buffer.encode()) +# file.close() +# os.rename(l_filename[0],l_filename[1]) +# except: +# self.error("write_array_do", +# "Unable to write "+l_filename[1]) + +#def set_ao_two_e_ints_df_ao_integrals_complex(self,df_ao_integrals_complex): +# rank = 5 +# dims = list(range(rank)) +# dims[0] = 2 +# dims[1] = self.ao_basis_ao_num_per_kpt +# dims[2] = self.ao_basis_ao_num_per_kpt +# dims[3] = self.ao_two_e_ints_df_num +# dims[4] = self.nuclei_kpt_pair_num +# +# dim_max = 1 +# for d in dims: +# dim_max *= d +# self.acquire_lock('ao_two_e_ints_df_ao_integrals_complex') +# try: +# self.write_array_do(self.path_ao_two_e_ints,'df_ao_integrals_complex', rank,dims,dim_max,df_ao_integrals_complex) +# +def test_write_df_ao(rank,dims,dim_max,flatdata): + with gzip.open('test_ao_df_ints.gz','w') as f: + f.write(f'{rank:3d}\n'.encode()) + for d in dims: + f.write(f'{d:20d} '.encode()) + f.write("\n".encode()) + for i in range(dim_max): + f.write(f'{flatdata[i]:25.15E}\n'.encode()) + return + +def save_array_do(ezfioname,subdir,data,chunksize=16384): + dims = list(reversed(data.shape)) + rank = len(dims) + flatdata = data.reshape(-1) + dim_max = 1 + for i in dims: + dim_max *= i + with gzip.open(os.path.join(ezfioname,subdir)+'.gz','wb') as f: + f.write(f'{rank:3d}\n'.encode()) + for d in dims: + f.write(f'{d:20d} '.encode()) + f.write("\n".encode()) + fmtstring = chunksize*'{:24.15E}\n' + for i in range(dim_max//chunksize): + #f.write((chunksize*'{:24.15E}\n').format(*flatdata[i*chunksize:(i+1)*chunksize]).encode()) + #f.write(fmtstring.format(*flatdata[i*chunksize:(i+1)*chunksize]).encode()) + f.write((''.join("%24.15E\n" % xi for xi in flatdata[i*chunksize:(i+1)*chunksize])).encode()) + print(f'{i/(dim_max//chunksize):7.3f}% complete') + rem = dim_max%chunksize + if rem: + f.write((rem*'{:24.15E}\n').format(*flatdata[-rem:]).encode()) + return + + + + def convert_mol(filename,qph5path): ezfio.set_file(filename) ezfio.set_nuclei_is_complex(False) @@ -387,7 +475,11 @@ def convert_kpts(filename,qph5path,qmcpack=True): # ezfio.set_ao_two_e_ints_df_ao_integrals_complex(dfao_cmplx0) #dfao_reim=qph5['ao_two_e_ints/df_ao_integrals'][()].tolist() dfao_reim=qph5['ao_two_e_ints/df_ao_integrals'][()] - ezfio.set_ao_two_e_ints_df_ao_integrals_complex(dfao_reim) + save_array_do(filename,'ao_two_e_ints/df_ao_integrals_complex',dfao_reim) + #ezfio.set_ao_two_e_ints_df_ao_integrals_complex(dfao_reim) + #dfao_dims = list(reversed(dfao_reim.shape)) + #test_write_df_ao(,5,dfao_dims,dfao_reim.size,dfao_reim.ravel()) + ezfio.set_ao_two_e_ints_io_df_ao_integrals('Read') if 'mo_two_e_ints' in qph5.keys():