fix some tiny issue on PR model with stress

MaterSim · Dec 19, 2022 · 95ae214 · 95ae214
1 parent d4710fd
commit 95ae214
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Showing 5 changed files with 13 additions and 7 deletions.
diff --git a/docs/conf.py b/docs/conf.py
@@ -19,13 +19,13 @@
 # -- Project information -----------------------------------------------------
 
 project = 'PyXtal_FF'
-copyright = '2019-2021, Qiang Zhu, Howard Yanxon, David Zagaceta'
+copyright = '2019-, Qiang Zhu, Howard Yanxon, David Zagaceta'
 author = 'Qiang Zhu, Howard Yanxon, David Zagaceta'
 
 # The short X.Y version
-version = '0.2.1'
+version = '0.2.2'
 # The full version, including alpha/beta/rc tags
-release = 'May 2022'
+release = 'Dec 2022'
 
 
 # -- General configuration ---------------------------------------------------

diff --git a/docs/index.rst b/docs/index.rst
@@ -2,7 +2,7 @@ PyXtal_FF
 ======================================
 The aim of PyXtalFF project is to provide an automated computational infrastructure to train the interatomic potentials for inorganic periodic systems from high-end quantum mechanical calculations.
 
-The current version is ``0.2.1`` at `GitHub <https://github.com/qzhu2017/pyxtal_ff>`_. 
+The current version is ``0.2.2`` at `GitHub <https://github.com/qzhu2017/pyxtal_ff>`_. 
 
 Expect updates upon request by `Qiang Zhu\'s group <https://qzhu2017.github.io>`_ at University of Nevada Las Vegas.
 

diff --git a/pyxtal_ff/calculator/__init__.py b/pyxtal_ff/calculator/__init__.py
@@ -56,6 +56,7 @@ def calculate(self, atoms=None,
 
         # pyxtal_ff and lammps uses: xx, yy, zz, xy, xz, yz
         # ase uses: xx, yy, zz, yz, xz, xy
+        # vasp uses: xx, yy, zz, xy, yz, zx
         # from eV/A^3 to GPa 
         self.results['stress_zbl'] = base_stress/units.GPa
         self.results['energy_zbl'] = base_energy

diff --git a/pyxtal_ff/models/polynomialregression.py b/pyxtal_ff/models/polynomialregression.py
@@ -141,7 +141,7 @@ def evaluate(self, data, figname):
                     _force.append(Force[m])
 
             if self.stress_coefficient and (db[str(i)]['group'] in self.stress_group):
-                true_stress = np.array(db[str(i)]['stress'])#.flat[[0,3,5,3,1,4,5,4,2]]
+                true_stress = np.ravel(db[str(i)]['stress'])#.flat[[0,3,5,3,1,4,5,4,2]]
                 Stress = np.ravel(Stress)
                 for m in range(len(true_stress)):
                     stress.append(true_stress[m])
@@ -707,6 +707,11 @@ def parse_features(self, data):
 
         for i in range(self.no_of_structures):
             data = db[str(i)]
+            #for key in data.keys():
+            #    if key in ['x', 'dxdr', 'rdxdr', 'seq', 'force']:
+            #        print(key, data[key].shape)
+            #    else:
+            #        print(key, data[key])
             #energy = np.array([data['energy']/len(data['elements'])])
             energy = np.array([data['energy']])
             w_energy = np.array([1.])
@@ -716,7 +721,7 @@ def parse_features(self, data):
                 w_force = np.array([self.force_coefficient]*len(force))
 
                 if self.stress_coefficient and (data['group'] in self.stress_group):     # energy + forces + stress
-                    stress = np.array(data['stress'])#.flat[[0,3,5,3,1,4,5,4,2]]
+                    stress = np.array(data['stress']).ravel()#.flat[[0,3,5,3,1,4,5,4,2]]
                     w_stress = np.array([self.stress_coefficient]*len(stress))
                     self.stress_components += 6
 

diff --git a/pyxtal_ff/version.py b/pyxtal_ff/version.py
@@ -1 +1 @@
-__version__ = '0.2.1'
+__version__ = '0.2.2'