def write_input(self, atoms, properties=None, system_changes=None): FileIOCalculator.write_input(self, atoms, properties, system_changes) struct = crys.atoms2struct(atoms) self.cell = common.str_arr(struct.cell) self.kpoints = pwscf.kpoints_str_pwin(kpts2mp(atoms, self.kpts)) if isinstance(self.pp, types.StringType): pseudos = ["%s.%s" %(sym, self.pp) for sym in struct.symbols_unique] else: assert len(self.pp) == struct.ntypat pseudos = [] for sym in struct.symbols_unique: for ppi in self.pp: if ppi.startswith(sym): pseudos.append(ppi) break assert len(pseudos) == struct.ntypat self.atspec = pwscf.atspec_str(symbols=struct.symbols_unique, masses=struct.mass_unique, pseudos=pseudos) self.atpos = pwscf.atpos_str(symbols=struct.symbols, coords=struct.coords_frac) self.natoms = struct.natoms self.ntyp = struct.ntypat if self.backup: for fn in [self.infile, self.outfile]: if os.path.exists(fn): common.backup(fn) common.file_write(self.infile, self.fill_infile_templ())
def write_input(self, atoms, properties=None, system_changes=None): FileIOCalculator.write_input(self, atoms, properties, system_changes) struct = crys.atoms2struct(atoms) self.cell = common.str_arr(struct.cell) self.kpoints = pwscf.kpoints_str_pwin(kpts2mp(atoms, self.kpts)) if isinstance(self.pp, bytes): pseudos = [ "%s.%s" % (sym, self.pp) for sym in struct.symbols_unique ] else: assert len(self.pp) == struct.ntypat pseudos = [] for sym in struct.symbols_unique: for ppi in self.pp: if ppi.startswith(sym): pseudos.append(ppi) break assert len(pseudos) == struct.ntypat self.atspec = pwscf.atspec_str(symbols=struct.symbols_unique, masses=struct.mass_unique, pseudos=pseudos) self.atpos = pwscf.atpos_str(symbols=struct.symbols, coords=struct.coords_frac) self.natoms = struct.natoms self.ntyp = struct.ntypat if self.backup: for fn in [self.infile, self.outfile]: if os.path.exists(fn): common.backup(fn) common.file_write(self.infile, self.fill_infile_templ())
def write_input(self, atoms, properties=None, system_changes=None): FileIOCalculator.write_input(self, atoms, properties, system_changes) if self.backup: for fn in [self.infile, self.outfile, self.dumpfile, self.structfile, self.logfile]: if os.path.exists(fn): common.backup(fn) common.file_write(self.infile, self.fill_infile_templ()) io.write_lammps(self.structfile, crys.atoms2struct(atoms), symbolsbasename=os.path.basename(self.structfile) + \ '.symbols')
def write_input(self, atoms, properties=None, system_changes=None): FileIOCalculator.write_input(self, atoms, properties, system_changes) if self.backup: for fn in [ self.infile, self.outfile, self.dumpfile, self.structfile, self.logfile ]: if os.path.exists(fn): common.backup(fn) common.file_write(self.infile, self.fill_infile_templ()) io.write_lammps(self.structfile, crys.atoms2struct(atoms), symbolsbasename=os.path.basename(self.structfile) + \ '.symbols')
def write_input(self, mode='a', backup=True, sleep=0, excl=True): """ Create calculation dir(s) for each parameter set and write input files based on ``templates``. Write sqlite database storing all relevant parameters. Write (bash) shell script to start all calculations (run locally or submitt batch job file, depending on ``machine.subcmd``). Parameters ---------- mode : str, optional Fine tune how to write input files (based on ``templates``) to calc dirs calc_foo/0/, calc_foo/1/, ... . Note that this doesn't change the base dir calc_foo at all, only the subdirs for each calc. {'a', 'w'} | 'a': Append mode (default). If a previous database is found, then | subsequent calculations are numbered based on the last 'idx'. | calc_foo/0 # old | calc_foo/1 # old | calc_foo/2 # new | calc_foo/3 # new | 'w': Write mode. The target dirs are purged and overwritten. Also, | the database (self.dbfn) is overwritten. Use this to | iteratively tune your inputs, NOT for working on already | present results! | calc_foo/0 # new | calc_foo/1 # new backup : bool, optional Before writing anything, do a backup of self.calc_dir if it already exists. sleep : int, optional For the script to start (submitt) all jobs: time in seconds for the shell sleep(1) commmand. excl : bool If in append mode, a file <calc_root>/excl_push with all indices of calculations from old revisions is written. Can be used with ``rsync --exclude-from=excl_push`` when pushing appended new calculations to a cluster. """ assert mode in ['a', 'w'], "Unknown mode: '%s'" %mode if os.path.exists(self.dbfn): if backup: common.backup(self.dbfn) if mode == 'w': os.remove(self.dbfn) have_new_db = not os.path.exists(self.dbfn) common.makedirs(self.calc_root) # this call creates a file ``self.dbfn`` if it doesn't exist sqldb = SQLiteDB(self.dbfn, table=self.db_table) # max_idx: counter for calc dir numbering revision = 0 if have_new_db: max_idx = -1 else: if mode == 'a': if sqldb.has_column('idx'): max_idx = sqldb.execute("select max(idx) from %s" \ %self.db_table).fetchone()[0] else: raise StandardError("database '%s': table '%s' has no " "column 'idx', don't know how to number calcs" %(self.dbfn, self.db_table)) if sqldb.has_column('revision'): revision = int(sqldb.get_single("select max(revision) \ from %s" %self.db_table)) + 1 elif mode == 'w': max_idx = -1 sql_records = [] hostnames = [] for imach, machine in enumerate(self.machines): hostnames.append(machine.hostname) calc_dir = pj(self.calc_root, self.calc_dir_prefix + \ '_%s' %machine.hostname) if os.path.exists(calc_dir): if backup: common.backup(calc_dir) if mode == 'w': common.system("rm -r %s" %calc_dir, wait=True) run_txt = "here=$(pwd)\n" for _idx, params in enumerate(self.params_lst): params = common.flatten(params) idx = max_idx + _idx + 1 calc_subdir = pj(calc_dir, str(idx)) extra_dct = \ {'revision': revision, 'study_name': self.study_name, 'idx': idx, 'calc_name' : self.study_name + "_run%i" %idx, } extra_params = [SQLEntry(key=key, sqlval=val) for key,val in \ extra_dct.iteritems()] # templates[:] to copy b/c they may be modified in Calculation calc = Calculation(machine=machine, templates=self.templates[:], params=params + extra_params, calc_dir=calc_subdir, ) if mode == 'w' and os.path.exists(calc_subdir): shutil.rmtree(calc_subdir) calc.write_input() run_txt += "cd %i && %s %s && cd $here && sleep %i\n" %(idx,\ machine.subcmd, machine.get_jobfile_basename(), sleep) if imach == 0: sql_records.append(calc.get_sql_record()) common.file_write(pj(calc_dir, 'run.sh'), run_txt) for record in sql_records: record['hostname'] = SQLEntry(sqlval=','.join(hostnames)) # for incomplete parameters: collect header parts from all records and # make a set = unique entries raw_header = [(key, entry.sqltype.upper()) for record in sql_records \ for key, entry in record.iteritems()] header = list(set(raw_header)) if have_new_db: sqldb.create_table(header) else: for record in sql_records: for key, entry in record.iteritems(): if not sqldb.has_column(key): sqldb.add_column(key, entry.sqltype.upper()) for record in sql_records: cmd = "insert into %s (%s) values (%s)"\ %(self.db_table, ",".join(record.keys()), ",".join(['?']*len(record.keys()))) sqldb.execute(cmd, tuple(entry.sqlval for entry in record.itervalues())) if excl and revision > 0 and sqldb.has_column('revision'): old_idx_lst = [str(x) for x, in sqldb.execute("select idx from calc where \ revision < ?", (revision,))] common.file_write(pj(self.calc_root, 'excl_push'), '\n'.join(old_idx_lst)) sqldb.finish()
def test_backup(): # file name = tempfile.mktemp(prefix='testfile', dir=testdir) file_write(name, 'foo') backup(name) assert os.path.exists(name + '.0') backup(name) assert os.path.exists(name + '.1') backup(name) assert os.path.exists(name + '.2') # dir name = tempfile.mktemp(prefix='testdir', dir=testdir) create_full_dir(name) backup(name) assert os.path.exists(name + '.0') backup(name) assert os.path.exists(name + '.1') backup(name) assert os.path.exists(name + '.2') # link to file filename = tempfile.mktemp(prefix='testfile', dir=testdir) linkname = tempfile.mktemp(prefix='testlink', dir=testdir) file_write(filename, 'foo') os.symlink(filename, linkname) backup(linkname) assert os.path.exists(linkname + '.0') assert os.path.isfile(linkname + '.0') assert file_read(linkname + '.0') == file_read(filename) # link to dir dirname = tempfile.mktemp(prefix='testdir', dir=testdir) linkname = tempfile.mktemp(prefix='testlink', dir=testdir) create_full_dir(dirname) os.symlink(dirname, linkname) backup(linkname) assert os.path.exists(linkname + '.0') assert os.path.isdir(linkname + '.0') for name in ['a', 'b', 'c']: assert file_read(pj(dirname, name)) == \ file_read(pj(linkname + '.0', name)) # prefix name = tempfile.mktemp(prefix='testfile', dir=testdir) file_write(name, 'foo') backup(name, prefix="-bak") assert os.path.exists(name + '-bak0') # nonexisting src, should silently pass filename = str(uuid.uuid4()) assert not os.path.exists(filename) backup(filename)
def write_input(self, mode='a', backup=True, sleep=0, excl=True): """ Create calculation dir(s) for each parameter set and write input files based on ``templates``. Write sqlite database storing all relevant parameters. Write (bash) shell script to start all calculations (run locally or submitt batch job file, depending on ``machine.subcmd``). Parameters ---------- mode : str, optional Fine tune how to write input files (based on ``templates``) to calc dirs calc_foo/0/, calc_foo/1/, ... . Note that this doesn't change the base dir calc_foo at all, only the subdirs for each calc. {'a', 'w'} | 'a': Append mode (default). If a previous database is found, then | subsequent calculations are numbered based on the last 'idx'. | calc_foo/0 # old | calc_foo/1 # old | calc_foo/2 # new | calc_foo/3 # new | 'w': Write mode. The target dirs are purged and overwritten. Also, | the database (self.dbfn) is overwritten. Use this to | iteratively tune your inputs, NOT for working on already | present results! | calc_foo/0 # new | calc_foo/1 # new backup : bool, optional Before writing anything, do a backup of self.calc_dir if it already exists. sleep : int, optional For the script to start (submitt) all jobs: time in seconds for the shell sleep(1) commmand. excl : bool If in append mode, a file <calc_root>/excl_push with all indices of calculations from old revisions is written. Can be used with ``rsync --exclude-from=excl_push`` when pushing appended new calculations to a cluster. """ assert mode in ['a', 'w'], "Unknown mode: '%s'" % mode if os.path.exists(self.dbfn): if backup: common.backup(self.dbfn) if mode == 'w': os.remove(self.dbfn) have_new_db = not os.path.exists(self.dbfn) common.makedirs(self.calc_root) # this call creates a file ``self.dbfn`` if it doesn't exist sqldb = SQLiteDB(self.dbfn, table=self.db_table) # max_idx: counter for calc dir numbering revision = 0 if have_new_db: max_idx = -1 else: if mode == 'a': if sqldb.has_column('idx'): max_idx = sqldb.execute("select max(idx) from %s" \ %self.db_table).fetchone()[0] else: raise Exception( "database '%s': table '%s' has no " "column 'idx', don't know how to number calcs" % (self.dbfn, self.db_table)) if sqldb.has_column('revision'): revision = int( sqldb.get_single("select max(revision) \ from %s" % self.db_table)) + 1 elif mode == 'w': max_idx = -1 sql_records = [] hostnames = [] for imach, machine in enumerate(self.machines): hostnames.append(machine.hostname) calc_dir = pj(self.calc_root, self.calc_dir_prefix + \ '_%s' %machine.hostname) if os.path.exists(calc_dir): if backup: common.backup(calc_dir) if mode == 'w': common.system("rm -r %s" % calc_dir, wait=True) run_txt = "here=$(pwd)\n" for _idx, params in enumerate(self.params_lst): params = common.flatten(params) idx = max_idx + _idx + 1 calc_subdir = pj(calc_dir, str(idx)) extra_dct = \ {'revision': revision, 'study_name': self.study_name, 'idx': idx, 'calc_name' : self.study_name + "_run%i" %idx, } extra_params = [SQLEntry(key=key, sqlval=val) for key,val in \ extra_dct.items()] # templates[:] to copy b/c they may be modified in Calculation calc = Calculation( machine=machine, templates=self.templates[:], params=params + extra_params, calc_dir=calc_subdir, ) if mode == 'w' and os.path.exists(calc_subdir): shutil.rmtree(calc_subdir) calc.write_input() run_txt += "cd %i && %s %s && cd $here && sleep %i\n" %(idx,\ machine.subcmd, machine.get_jobfile_basename(), sleep) if imach == 0: sql_records.append(calc.get_sql_record()) common.file_write(pj(calc_dir, 'run.sh'), run_txt) for record in sql_records: record['hostname'] = SQLEntry(sqlval=','.join(hostnames)) # for incomplete parameters: collect header parts from all records and # make a set = unique entries raw_header = [(key, entry.sqltype.upper()) for record in sql_records \ for key, entry in record.items()] header = list(set(raw_header)) if have_new_db: sqldb.create_table(header) else: for record in sql_records: for key, entry in record.items(): if not sqldb.has_column(key): sqldb.add_column(key, entry.sqltype.upper()) for record in sql_records: cmd = "insert into %s (%s) values (%s)"\ %(self.db_table, ",".join(list(record.keys())), ",".join(['?']*len(list(record.keys())))) sqldb.execute(cmd, tuple(entry.sqlval for entry in record.values())) if excl and revision > 0 and sqldb.has_column('revision'): old_idx_lst = [ str(x) for x, in sqldb.execute( "select idx from calc where \ revision < ?", ( revision, )) ] common.file_write(pj(self.calc_root, 'excl_push'), '\n'.join(old_idx_lst)) sqldb.finish()
def test_backup(): # file name = tempfile.mktemp(prefix='testfile', dir=testdir) file_write(name, 'foo') backup(name) assert os.path.exists(name + '.0') backup(name) assert os.path.exists(name + '.1') backup(name) assert os.path.exists(name + '.2') # dir name = tempfile.mktemp(prefix='testdir', dir=testdir) create_full_dir(name) backup(name) assert os.path.exists(name + '.0') backup(name) assert os.path.exists(name + '.1') backup(name) assert os.path.exists(name + '.2') # link to file filename = tempfile.mktemp(prefix='testfile', dir=testdir) linkname = tempfile.mktemp(prefix='testlink', dir=testdir) file_write(filename, 'foo') os.symlink(filename, linkname) backup(linkname) assert os.path.exists(linkname + '.0') assert os.path.isfile(linkname + '.0') assert file_read(linkname + '.0') == file_read(filename) # link to dir dirname = tempfile.mktemp(prefix='testdir', dir=testdir) linkname = tempfile.mktemp(prefix='testlink', dir=testdir) create_full_dir(dirname) os.symlink(dirname, linkname) backup(linkname) assert os.path.exists(linkname + '.0') assert os.path.isdir(linkname + '.0') for name in ['a', 'b', 'c']: assert file_read(pj(dirname, name)) == \ file_read(pj(linkname + '.0', name)) # prefix name = tempfile.mktemp(prefix='testfile', dir=testdir) file_write(name, 'foo') backup(name, prefix="-bak") assert os.path.exists(name + '-bak0')