From e2cb25c4802c9b50239b9ab1ad48f204cf5c828e Mon Sep 17 00:00:00 2001
From: Atsushi Togo <atz.togo@gmail.com>
Date: Tue, 7 Aug 2018 14:57:37 +0900
Subject: [PATCH] Minor update for QHA

---
 scripts/phonopy-qha | 55 +++++++++++++++++++--------------------------
 1 file changed, 23 insertions(+), 32 deletions(-)

diff --git a/scripts/phonopy-qha b/scripts/phonopy-qha
index fd63422e..64a91b9d 100755
--- a/scripts/phonopy-qha
+++ b/scripts/phonopy-qha
@@ -49,7 +49,7 @@ def get_options():
                         is_graph_plot=False,
                         is_graph_save=False,
                         is_bulk_modulus_only=False,
-                        read_efe_file=False,
+                        efe_file=None,
                         eos="vinet",
                         thin_number=10,
                         tmax=1000.0)
@@ -69,9 +69,9 @@ def get_options():
         "--pressure", dest="pressure", type=float,
         help="Pressure in GPa")
     parser.add_argument(
-        "--read-efe", "--read-electronic-free-energy",
-        dest="read_efe_file", action="store_true",
-        help="Read electronic free energies from file instead of v-e data")
+        "--efe", "--electronic-free-energy",
+        dest="efe_file", nargs=1,
+        help="Read electronic free energies at temperatures and volumes")
     parser.add_argument(
         "-s", "--save", dest="is_graph_save", action="store_true",
         help="Save plot data in pdf")
@@ -105,8 +105,8 @@ def main(args):
 
     # Show bulk modulus of v-e data
     if args.is_bulk_modulus_only:
-        if args.read_efe_file:
-            print("--read-efe optin can't be used with -b option")
+        if args.efe_file:
+            print("--efe optin can't be used with -b option")
             sys.exit(1)
 
         volumes, electronic_energies = read_v_e(args.filenames[0])
@@ -126,34 +126,30 @@ def main(args):
     ########################
     # Read data from files #
     ########################
-    if args.read_efe_file:
-        _temperatures, electronic_energies = read_efe(args.filenames[0])
-    else:
-        volumes, electronic_energies = read_v_e(args.filenames[0])
-        electronic_energies += volumes * args.pressure / EVAngstromToGPa
-        # Check number of files in e-v.dat case
-        if not args.read_efe_file and len(volumes) != len(args.filenames[1:]):
-            print("The number of thermal_properites.yaml files (%d) "
-                  "is inconsisten with" % len(args.filenames[1:]))
-            print("the number of e-v data (%d)." % len(volumes))
+    volumes, electronic_energies = read_v_e(args.filenames[0])
+    electronic_energies += volumes * args.pressure / EVAngstromToGPa
+    # Check number of files in e-v.dat case
+    if len(volumes) != len(args.filenames[1:]):
+        print("The number of thermal_properites.yaml files (%d) "
+              "is inconsisten with" % len(args.filenames[1:]))
+        print("the number of e-v data (%d)." % len(volumes))
+        sys.exit(1)
+
+    if args.efe_file:
+        _temperatures, electronic_energies = read_efe(args.efe_file[0])
+        if len(volumes) != electronic_energies.shape[1]:
+            print("%s and %s are inconsistent for the volume points."
+                  % (args.filenames[0], args.efe_file[0]))
             sys.exit(1)
 
     (temperatures,
      cv,
      entropy,
      fe_phonon,
-     _volumes,
      num_modes,
      num_integrated_modes) = read_thermal_properties_yaml(args.filenames[1:])
 
-    if args.read_efe_file:
-        if len(_volumes) == electronic_energies.shape[1]:
-            volumes = np.array(_volumes)
-        else:
-            print("Unit cell volumes could not be collected from "
-                  "thermal_properties.yaml files. Use the latset phonopy-qha "
-                  "and re-calculate thermal_properties.yaml's")
-            sys.exit(1)
+    if args.efe_file:
         if ((len(temperatures) >= len(_temperatures) and
             (np.abs(temperatures[:len(_temperatures)] - _temperatures)
              > 1e-5).any()) or
@@ -162,12 +158,7 @@ def main(args):
              > 1e-5).any())):
             print("Inconsistency is found in temperatures in %s and "
                   "thermal_properties.yaml files." % args.filenames[0])
-    else:
-        if len(_volumes) == len(volumes):
-            if (np.abs(volumes - _volumes) > 1e-4).any():
-                print("Inconsistency is found in unti cell volumes in %s "
-                      "and thermal_properties.yaml files" % args.filenames[0])
-                sys.exit(1)
+            sys.exit(1)
 
     ########################################################
     # Treatment of thermal properties with imaginary modes #
@@ -181,7 +172,7 @@ def main(args):
     else:
         indices = range(len(volumes))
 
-    if args.read_efe_file:
+    if args.efe_file:
         electronic_energies = electronic_energies[:, indices]
     else:
         electronic_energies = electronic_energies[indices]