MD stuff

abipy/dynamics/cpx.py

@@ -79,6 +79,11 @@ def df(self) -> pd.DataFrame:
         df = pd.read_csv(self.filepath, delim_whitespace=True, skiprows=1, names=names)
         return df
 
+    @lazy_property
+    def times(self):
+        """Array with times in ps units."""
+        return evp.df["tps(ps)"].values
+
     def to_string(self, verbose=0) -> str:
         """String representation with verbosity level verbose."""
         lines = []; app = lines.append

abipy/electrons/ebands.py

@@ -2047,7 +2047,7 @@ def plot_ejdosvc(self, vrange, crange, method="gaussian", step=0.1, width=0.2, c
             method: String defining the method.
             step: Energy step (eV) of the linear mesh.
             width: Standard deviation (eV) of the gaussian.
-            colormap: Have a look at the colormaps here and decide which one you like:
+            colormap: Color map. Have a look at the colormaps here and decide which one you like:
                 http://matplotlib.sourceforge.net/examples/pylab_examples/show_colormaps.html
             cumulative: True for cumulative plots (default).
             ax: |matplotlib-Axes| or None if a new figure should be created.
@@ -2449,7 +2449,7 @@ def plot_scatter3d(self, band, spin=0, e0="fermie", colormap="jet", ax=None, **k
                 - ``fermie``: shift all eigenvalues to have zero energy at the Fermi energy (``self.fermie``).
                 -  Number e.g ``e0 = 0.5``: shift all eigenvalues to have zero energy at 0.5 eV
                 -  None: Don't shift energies, equivalent to ``e0 = 0``.
-            colormap: Have a look at the colormaps here and decide which one you like:
+            colormap: Color map. Have a look at the colormaps here and decide which one you like:
                 <http://matplotlib.sourceforge.net/examples/pylab_examples/show_colormaps.html>
             ax: matplotlib :class:`Axes3D` or None if a new figure should be created.
         """

abipy/ml/aseml.py

@@ -45,6 +45,7 @@
 from ase.md.velocitydistribution import (MaxwellBoltzmannDistribution, Stationary, ZeroRotation)
 from abipy.core import Structure
 from abipy.tools.iotools import workdir_with_prefix, PythonScript, yaml_safe_load_path
+from abipy.tools.typing import Figure
 from abipy.tools.printing import print_dataframe
 from abipy.tools.serialization import HasPickleIO
 from abipy.abio.enums import StrEnum, EnumMixin
@@ -1172,6 +1173,7 @@ def install_nn_names(nn_names="all", update=False, verbose=0) -> None:
     def pip_install(nn_name) -> int:
         from subprocess import call
         cmd = f"python -m pip install {nn_name}"
+        #print("About to execute", cmd)
         try:
             retcode = call(cmd, shell=True)
             if retcode < 0:
@@ -1187,18 +1189,23 @@ def pip_install(nn_name) -> int:
         "alignn",
     ]
 
-    nn_names = CalcBuilder.ALL_NN_TYPES if nn_names == "all" else list_strings(nn_names)
+    nn_names == list_strings(nn_names)
+    if "all" in nn_names: nn_names = CalcBuilder.ALL_NN_TYPES 
     installed, versions = get_installed_nn_names(verbose=verbose, printout=False)
 
     for name in nn_names:
+        #print(f"About to install nn_name={name}")
         if name in black_list:
             print("Cannot install {name} with pip!")
             continue
         if name in installed:
             if not update:
                 print("{name} is already installed!. Use update to update the package")
                 continue
-            print("Upgradig {name}")
+            print("Upgrading: {name}")
+        if name not in CalcBuilder.ALL_NN_TYPES:
+            print(f"Ignoring unknown {name=}")
+            continue
 
         pip_install(name)
 
@@ -1763,7 +1770,6 @@ def restart_md(traj_filepath, atoms, verbose) -> tuple[bool, int]:
 
 
 from abipy.core.mixins import TextFile, NotebookWriter
-#class AseMdLog(TextFile, NotebookWriter):
 class AseMdLog(TextFile):
     """
     Postprocessing tool for the log file produced by ASE MD.
@@ -1782,6 +1788,7 @@ def df(self) -> pd.DataFrame:
         # Here we implement the logic required to take into account a possible restart.
         begin_restart = False
         d = {}
+        add_time = 0.0
         with open(self.filepath, mode="rt") as fh:
             for i, line in enumerate(fh):
                 if i == 0:
@@ -1795,7 +1802,6 @@ def df(self) -> pd.DataFrame:
                     begin_restart = True
                     continue
 
-                add_time = 0.0
                 if begin_restart:
                     # First iteration after restart. Set add_time and kkip it.
                     begin_restart = False
@@ -1901,7 +1907,7 @@ def run(self) -> None:
             loginterval=self.loginterval,
             ensemble   =self.ensemble,
             nn_name    =self.nn_name,
-            workdir    =self.workdir,
+            workdir    =str(self.workdir),
             verbose    =self.verbose,
         )
         self.write_json("md.json", md_dict, info="JSON file with ASE MD parameters")

abipy/scripts/abiml.py

@@ -642,7 +642,7 @@ def show(ctx, verbose):
 @click.option('-v', '--verbose', count=True, help="Verbosity level")
 def install(ctx, nn_names, update, verbose):
     """
-    Install NN potentials in the environment using pip
+    Install NN potentials in the environment using pip.
     """
     aseml.install_nn_names(nn_names=nn_names, update=update, verbose=verbose)
     installed, versions = aseml.get_installed_nn_names(verbose=verbose, printout=True)

abipy/scripts/abips.py

@@ -121,7 +121,7 @@ def abips_install(options) -> int:
         return 0
 
     print("The following pseudopotential repositories will be installed:")
-    print(tabulate_repos(repos, verbose=options.verbose))
+    print(tabulate_repos(repos, verbose=options.verbose), "\n")
     #if not options.yes and cli.user_wants_to_abort(): return 2
 
     for repo in repos:

abipy/tools/plotting.py

@@ -253,12 +253,41 @@ def set_ax_xylabels(ax, xlabel: str, ylabel: str, exchange_xy: bool = False) ->
     ax.set_ylabel(ylabel)
 
 
+def set_logscale(ax_or_axlist, xy_log) -> None:
+    """
+    Activate logscale
+
+    Args:
+        ax_or_axlist: Axes or list of axes.
+        xy_log:
+            None or empty string -> Use linear scale.
+            x                    -> Use log scale on x-axis
+            xy                   -> Use log scale on x- and y-axis
+            x:semilog            -> Use semilog scale on x-axis.
+    """
+    if not xy_log: return
+
+    # Parse xy_log string.
+    xy, log_type = xy_log, "log"
+    if ":" in xy_log:
+        xy, log_type = xy_log.split(":")
+
+    ax_list = [ax_or_axlist] if not duck.is_listlike(ax_or_axlist) else ax_or_axlist
+
+    for ix, ax in enumerate(ax_list):
+        if "x" in xy:
+            ax.set_xscale(log_type)
+        if "y" in xy:
+            ax.set_yscale(log_type)
+
+
 def set_ticks_fontsize(ax_or_axlist, fontsize: int, xy_string="xy") -> None:
     """
     Set tick properties for one axis or a list of axis.
 
     Args:
-        xy_string: "x" to share x-axis, "xy" for both
+        ax_or_axlist: Axes or list of axes.
+        xy_string: "x" to share x-axis, "xy" for both.
     """
     ax_list = [ax_or_axlist] if not duck.is_listlike(ax_or_axlist) else ax_or_axlist