From a8acd7063c9fc4283ce378403a2741bc98623731 Mon Sep 17 00:00:00 2001
From: knc6 <writetokamal.1989@gmail.com>
Date: Sun, 31 Mar 2024 11:25:39 -0400
Subject: [PATCH] Update lammps.

---
 jarvis/io/lammps/inputs.py    |  8 ++++----
 jarvis/io/lammps/outputs.py   |  8 ++++++--
 jarvis/tasks/lammps/lammps.py | 14 +++++++++-----
 3 files changed, 19 insertions(+), 11 deletions(-)

diff --git a/jarvis/io/lammps/inputs.py b/jarvis/io/lammps/inputs.py
index 3e778087..c29ed9a9 100644
--- a/jarvis/io/lammps/inputs.py
+++ b/jarvis/io/lammps/inputs.py
@@ -61,10 +61,10 @@ def atoms_to_lammps(self, atoms, origin=(0, 0, 0)):
         xhi = a + xlo
         m = atoms.lattice._lat
         xy = np.dot(m[1], m[0] / a)
-        yhi = np.sqrt(b ** 2 - xy ** 2) + ylo
+        yhi = np.sqrt(b**2 - xy**2) + ylo
         xz = np.dot(m[2], m[0] / a)
         yz = (np.dot(m[1], m[2]) - xy * xz) / (yhi - ylo)
-        zhi = np.sqrt(c ** 2 - xz ** 2 - yz ** 2) + zlo
+        zhi = np.sqrt(c**2 - xz**2 - yz**2) + zlo
         rot_matrix = np.linalg.solve(
             [[xhi - xlo, 0, 0], [xy, yhi - ylo, 0], [xz, yz, zhi - zlo]], m
         )
@@ -94,7 +94,7 @@ def read_data(
         filename="lammps.data",
         element_order=[],
         potential_file="pot.mod",
-        verbose=True,
+        verbose=False,
         has_charges=True,
     ):
         """Read Lammps data file."""
@@ -179,7 +179,7 @@ def read_data(
                     y[j] = float((lines[i + j + 2]).split()[it + 2])
                     z[j] = float((lines[i + j + 2]).split()[it + 3])
                     coords.append([x[j], y[j], z[j]])
-                    print(coords[-1])
+                    # print(coords[-1])
         f.close()
         # print ("info",(typ),'coo',(coords),'latt',lat)
         typ_sp = [str(i, "utf-8") for i in typ]
diff --git a/jarvis/io/lammps/outputs.py b/jarvis/io/lammps/outputs.py
index da4a4a86..32c72e1a 100644
--- a/jarvis/io/lammps/outputs.py
+++ b/jarvis/io/lammps/outputs.py
@@ -1,10 +1,10 @@
 """Function to analze LAMMPS output."""
+
 import numpy as np
 import glob
 import os
 from jarvis.analysis.elastic.tensor import ElasticTensor
 from jarvis.io.lammps.inputs import LammpsData
-from jarvis.io.phonopy.outputs import bandstructure_plot, total_dos
 from jarvis.core.atoms import Atoms
 
 
@@ -251,6 +251,8 @@ def parse_material_calculation_folder(
 
     with optimization, vacancy, phonon, surface etc.
     """
+    from jarvis.io.phonopy.outputs import bandstructure_plot, total_dos
+
     cwd = os.getcwd()
     jid_file = os.path.join(path, "JARVISFF-ID")
     if os.path.exists(jid_file):
@@ -375,7 +377,9 @@ def parse_material_calculation_folder(
     return info
 
 
-def parse_full_ff_folder(path="Mishin-Ni-Al-2009.eam.alloy_nist",):
+def parse_full_ff_folder(
+    path="Mishin-Ni-Al-2009.eam.alloy_nist",
+):
     """Parse complete FF calculation folder."""
     cwd = os.getcwd()
     os.chdir(path)
diff --git a/jarvis/tasks/lammps/lammps.py b/jarvis/tasks/lammps/lammps.py
index bcf6c122..16c9cb90 100644
--- a/jarvis/tasks/lammps/lammps.py
+++ b/jarvis/tasks/lammps/lammps.py
@@ -142,11 +142,15 @@ def phonons(
         self, atoms=None, lammps_cmd="", enforce_c_size=15.0, parameters={}
     ):
         """Make Phonon calculation setup."""
-        from phonopy import Phonopy
-        from phonopy.file_IO import (
-            #    parse_FORCE_CONSTANTS,
-            write_FORCE_CONSTANTS,
-        )
+        try:
+         from phonopy import Phonopy
+         from phonopy.file_IO import (
+             #    parse_FORCE_CONSTANTS,
+             write_FORCE_CONSTANTS,
+         )
+        except Exception as exp:
+           print('Phonopy check',exp)
+           pass
 
         bulk = atoms.phonopy_converter()