Merge pull request 'feat/qcd2_par' (#27) from feat/qcd2_par into develop

Reviewed-on: https://www.kuhl-mann.de/git/git/jkuhl/corrlib/pulls/27

corrlib/input/openQCD.py

@@ -4,9 +4,12 @@ import os
 import fnmatch
 from typing import Any, Optional
 from pathlib import Path
+from ..pars.openQCD import ms1
+from ..pars.openQCD import qcd2
 
 
-def read_ms1_param(path: Path, project: str, file_in_project: str) -> dict[str, Any]:
+
+def load_ms1_infile(path: Path, project: str, file_in_project: str) -> dict[str, Any]:
     """
     Read the parameters for ms1 measurements from a parameter file in the project.
 
@@ -70,7 +73,7 @@ def read_ms1_param(path: Path, project: str, file_in_project: str) -> dict[str,
     return param
 
 
-def read_ms3_param(path: Path, project: str, file_in_project: str) -> dict[str, Any]:
+def load_ms3_infile(path: Path, project: str, file_in_project: str) -> dict[str, Any]:
     """
     Read the parameters for ms3 measurements from a parameter file in the project.
 
@@ -304,3 +307,51 @@ def extract_t1(path: Path, project: str, dir_in_project: str, param: dict[str, A
     t1_dict[param["type"]] = {}
     t1_dict[param["type"]][pars] = t0
     return t1_dict
+
+
+def load_qcd2_pars(path: Path, project: str, file_in_project: str)  -> dict[str, Any]:
+    """
+    Thin wrapper around read_qcd2_par_file, getting the file before reading.
+
+    Parameters
+    ----------
+    path: Path
+        Path of the corrlib repository.
+    project: str
+        UUID of the project of the parameter-file.
+    file_in_project: str
+        The loaction of the file in the project directory.
+
+    Returns
+    -------
+    par_dict: dict
+        The dict with the parameters read from the .par-file.
+    """
+    fname = path / "projects" / project / file_in_project
+    ds = os.path.join(path, "projects", project)
+    dl.get(fname, dataset=ds)
+    return qcd2.read_qcd2_par_file(fname)
+
+
+def load_ms1_parfile(path: Path, project: str, file_in_project: str)  -> dict[str, Any]:
+    """
+    Thin wrapper around read_qcd2_ms1_par_file, getting the file before reading.
+
+    Parameters
+    ----------
+    path: Path
+        Path of the corrlib repository.
+    project: str
+        UUID of the project of the parameter-file.
+    file_in_project: str
+        The loaction of the file in the project directory.
+
+    Returns
+    -------
+    par_dict: dict
+        The dict with the parameters read from the .par-file.
+    """
+    fname = path / "projects" / project / file_in_project
+    ds = os.path.join(path, "projects", project)
+    dl.get(fname, dataset=ds)
+    return ms1.read_qcd2_ms1_par_file(fname)

corrlib/meas_io.py

@@ -74,7 +74,10 @@ def write_measurement(path: Path, ensemble: str, measurement: dict[str, dict[str
             ms_type = list(measurement.keys())[0]
             if ms_type == 'ms1':
                 if parameter_file is not None:
-                    parameters = openQCD.read_ms1_param(path, uuid, parameter_file)
+                    if parameter_file.endswith(".ms1.in"):
+                        parameters = openQCD.load_ms1_infile(path, uuid, parameter_file)
+                    elif parameter_file.endswith(".ms1.par"):
+                        parameters = openQCD.load_ms1_parfile(path, uuid, parameter_file)
                 else:
                     raise Exception("Need parameter file for this code!")
                 pars = {}
@@ -88,7 +91,7 @@ def write_measurement(path: Path, ensemble: str, measurement: dict[str, dict[str
                     pars[subkey] = json.dumps(parameters["rw_fcts"][i])
             elif ms_type in ['t0', 't1']:
                 if parameter_file is not None:
-                    parameters = openQCD.read_ms3_param(path, uuid, parameter_file)
+                    parameters = openQCD.load_ms3_infile(path, uuid, parameter_file)
                 else:
                     parameters = {}
                     for rwp in ["integrator", "eps", "ntot", "dnms"]:

corrlib/pars/openQCD/__init__.py

@@ -0,0 +1,3 @@
+
+from . import ms1 as ms1
+from . import qcd2 as qcd2

corrlib/pars/openQCD/flags.py

@@ -0,0 +1,59 @@
+"""
+Reconstruct the outputs of flags.
+"""
+
+import struct
+from typing import Any, BinaryIO
+
+# lat_parms.c
+def lat_parms_write_lat_parms(fp: BinaryIO) -> dict[str, Any]:
+        """
+        NOTE: This is a duplcation from qcd2.
+        Unpack the lattice parameters written by write_lat_parms.
+        """
+        lat_pars = {}
+        t = fp.read(16)
+        lat_pars["N"] = list(struct.unpack('iiii', t)) # lattice extends
+        t = fp.read(8)
+        nk, isw = struct.unpack('ii', t) # number of kappas and isw parameter
+        lat_pars["nk"] = nk
+        lat_pars["isw"] = isw
+        t = fp.read(8)
+        lat_pars["beta"] = struct.unpack('d', t)[0] # beta
+        t = fp.read(8)
+        lat_pars["c0"] = struct.unpack('d', t)[0]
+        t = fp.read(8)
+        lat_pars["c1"] = struct.unpack('d', t)[0]
+        t = fp.read(8)
+        lat_pars["csw"] = struct.unpack('d', t)[0] # csw factor
+        kappas = []
+        m0s = []
+        # read kappas
+        for ik in range(nk):
+            t = fp.read(8)
+            kappas.append(struct.unpack('d', t)[0])
+            t = fp.read(8)
+            m0s.append(struct.unpack('d', t)[0])
+        lat_pars["kappas"] = kappas
+        lat_pars["m0s"] = m0s
+        return lat_pars
+
+
+def lat_parms_write_bc_parms(fp: BinaryIO) -> dict[str, Any]:
+        """
+        NOTE: This is a duplcation from qcd2.
+        Unpack the boundary parameters written by write_bc_parms.
+        """
+        bc_pars: dict[str, Any] = {}
+        t = fp.read(4)
+        bc_pars["type"] = struct.unpack('i', t)[0] # type of hte boundaries
+        t = fp.read(104)
+        bc_parms = struct.unpack('d'*13, t)
+        bc_pars["cG"] = list(bc_parms[:2]) # boundary gauge field improvement
+        bc_pars["cF"] = list(bc_parms[2:4]) # boundary fermion field improvement
+        phi: list[list[float]] = [[], []]
+        phi[0] = list(bc_parms[4:7])
+        phi[1] = list(bc_parms[7:10])
+        bc_pars["phi"] = phi
+        bc_pars["theta"] = list(bc_parms[10:])
+        return bc_pars

corrlib/pars/openQCD/ms1.py

@@ -0,0 +1,30 @@
+from . import flags
+
+from typing import Any
+from pathlib import Path
+
+
+def read_qcd2_ms1_par_file(fname: Path) -> dict[str, dict[str, Any]]:
+    """
+    The subroutines written here have names according to the openQCD programs and functions that write out the data.
+    Parameters
+    ----------
+    fname: Path
+        Location of the parameter file.
+
+    Returns
+    -------
+    par_dict: dict
+        Dictionary holding the parameters specified in the given file.
+    """
+
+    with open(fname, "rb") as fp:
+        lat_par_dict = flags.lat_parms_write_lat_parms(fp)
+        bc_par_dict = flags.lat_parms_write_bc_parms(fp)
+        fp.close()
+    par_dict = {}
+    par_dict["lat"] = lat_par_dict
+    par_dict["bc"] = bc_par_dict
+    return par_dict
+
+

corrlib/pars/openQCD/qcd2.py

@@ -0,0 +1,29 @@
+from . import flags
+
+from pathlib import Path
+from typing import Any
+
+
+def read_qcd2_par_file(fname: Path) -> dict[str, dict[str, Any]]:
+    """
+    The subroutines written here have names according to the openQCD programs and functions that write out the data.
+
+    Parameters
+    ----------
+    fname: Path
+        Location of the parameter file.
+
+    Returns
+    -------
+    par_dict: dict
+        Dictionary holding the parameters specified in the given file.
+    """
+
+    with open(fname, "rb") as fp:
+        lat_par_dict = flags.lat_parms_write_lat_parms(fp)
+        bc_par_dict = flags.lat_parms_write_bc_parms(fp)
+        fp.close()
+    par_dict = {}
+    par_dict["lat"] = lat_par_dict
+    par_dict["bc"] = bc_par_dict
+    return par_dict

corrlib/toml.py

@@ -192,12 +192,16 @@ def import_toml(path: Path, file: str, copy_file: bool=True) -> None:
 
         elif project['code'] == 'openQCD':
             if md['measurement'] == 'ms1':
-                param = openQCD.read_ms1_param(path, uuid, md['param_file'])
+                parameter_file = md['param_file']
+                if parameter_file.endswith(".ms1.in"):
+                    param = openQCD.load_ms1_infile(path, uuid, parameter_file)
+                elif parameter_file.endswith(".ms1.par"):
+                    param = openQCD.load_ms1_parfile(path, uuid, parameter_file)
                 param['type'] = 'ms1'
                 measurement = openQCD.read_rwms(path, uuid, md['path'], param, md["prefix"], version=md["version"], names=md['names'], files=md['files'])
             elif md['measurement'] == 't0':
                 if 'param_file' in md:
-                    param = openQCD.read_ms3_param(path, uuid, md['param_file'])
+                    param = openQCD.load_ms3_infile(path, uuid, md['param_file'])
                 else:
                     param = {}
                     for rwp in ["integrator", "eps", "ntot", "dnms"]:
@@ -207,7 +211,7 @@ def import_toml(path: Path, file: str, copy_file: bool=True) -> None:
                                                  fit_range=int(md.get('fit_range', 5)), postfix=str(md.get('postfix', '')), names=md.get('names', []), files=md.get('files', []))
             elif md['measurement'] == 't1':
                 if 'param_file' in md:
-                    param = openQCD.read_ms3_param(path, uuid, md['param_file'])
+                    param = openQCD.load_ms3_infile(path, uuid, md['param_file'])
                 param['type'] = 't1'
                 measurement = openQCD.extract_t1(path, uuid, md['path'], param, str(md["prefix"]), int(md["dtr_read"]), int(md["xmin"]), int(md["spatial_extent"]),
                                                  fit_range=int(md.get('fit_range', 5)), postfix=str(md.get('postfix', '')), names=md.get('names', []), files=md.get('files', []))