Remove pyscal2

.github/workflows/testing.yml

@@ -48,3 +48,5 @@ jobs:
         pip install pytest
         pip install pytest-cov
         pytest tests/
+        cd examples/example_01
+        #calphy_kernel -i input.yaml -k 0 -s True

calphy/alchemy.py

@@ -24,7 +24,6 @@
 import numpy as np
 import yaml
 
-import pyscal.traj_process as ptp
 from calphy.integrators import *
 import calphy.lattice as pl
 import calphy.helpers as ph

calphy/helpers.py

@@ -22,16 +22,18 @@
 """
 
 import os
-from pylammpsmpi import LammpsLibrary
+import shutil
+import warnings
 import logging
 import numpy as np
+
+from pylammpsmpi import LammpsLibrary
 from lammps import lammps
-import calphy.lattice as pl
-import shutil
-import pyscal.core as pc
 from ase.io import read, write
-from pyscal.trajectory import Trajectory
-import warnings
+
+import calphy.lattice as pl
+import pyscal3.core as pc
+from pyscal3.trajectory import Trajectory
 
 class LammpsScript:
     def __init__(self):
@@ -329,15 +331,15 @@ def compute_msd(lmp, options):
 
 
 def find_solid_fraction(file):
-    sys = pc.System()
-    sys.read_inputfile(file)
+    sys = pc.System(file)
     try:
-        sys.find_neighbors(method="cutoff", cutoff=0)
+        sys.find.neighbors(method="cutoff", cutoff=0)
     except RuntimeError:
-        sys.find_neighbors(
+        sys.find.neighbors(
             method="cutoff", cutoff=5.0
         )  # Maybe add value as convergence param?
-    solids = sys.find_solids()
+    sys.find.solids()
+    solids = np.sum(sys.atoms.solid)
     return solids
 
 

calphy/integrators.py

@@ -30,7 +30,7 @@
 from calphy.splines import splines, sum_spline1, sum_spline25, sum_spline50, sum_spline75, sum_spline100
 from scipy.integrate import cumtrapz
 from tqdm import tqdm
-import pyscal.core as pc
+import pyscal3.core as pc
 from ase.io import read
 
 #Constants
@@ -356,12 +356,10 @@ def integrate_dcc(folder1, folder2, nsims=1, scale_energy=True,
     """
 
     #get number of atoms
-    sys = pc.System()
-    sys.read_inputfile(os.path.join(folder1, "traj.equilibration_stage1.dat"))
+    sys = pc.System(os.path.join(folder1, "traj.equilibration_stage1.dat"))
     natoms1 = int(sys.natoms)
 
-    sys = pc.System()
-    sys.read_inputfile(os.path.join(folder2, "traj.equilibration_stage1.dat"))
+    sys = pc.System(os.path.join(folder2, "traj.equilibration_stage1.dat"))
     natoms2 = int(sys.natoms)
 
     #get temp and pressure

calphy/lattice.py

@@ -25,7 +25,7 @@
 import os
 from pylammpsmpi import LammpsLibrary
 import numpy as np
-import pyscal.core as pc
+import pyscal3.core as pc
 from ase.io import read
 
 """
@@ -88,8 +88,7 @@ def get_lattice(symbol, lat):
 def check_dump_file(infile):
     try:
         #now use pyscal to read it in,
-        sys = pc.System()
-        sys.read_inputfile(infile)
+        sys = pc.System(infile)
         atoms = sys.atoms
         natoms = len(atoms)
         types = [atom.type for atom in atoms]
@@ -122,8 +121,7 @@ def check_data_file(infile, script_mode=False):
             trajfile = read(infile, format='lammps-data', style='atomic')
             format = 'ase'
         #now use pyscal to read it in,
-        sys = pc.System()
-        sys.read_inputfile(trajfile, format=format)
+        sys = pc.System(trajfile, format=format)
         atoms = sys.atoms
         types = [atom.type for atom in atoms]
         xx, xxcounts = np.unique(types, return_counts=True)

calphy/liquid.py

@@ -25,7 +25,6 @@
 import yaml
 
 from calphy.integrators import *
-import pyscal.traj_process as ptp
 import calphy.lattice as pl
 import calphy.helpers as ph
 import calphy.phase as cph

calphy/phase.py

@@ -29,7 +29,7 @@
 import yaml
 import copy
 
-import pyscal.traj_process as ptp
+import pyscal3.traj_process as ptp
 from calphy.integrators import *
 import calphy.lattice as pl
 import calphy.helpers as ph

calphy/solid.py

@@ -26,7 +26,6 @@
 import copy
 import sys
 
-import pyscal.traj_process as ptp
 from calphy.integrators import *
 import calphy.lattice as pl
 import calphy.helpers as ph

environment-docs.yml

@@ -9,7 +9,7 @@ dependencies:
   - openmpi 
   - mpi4py
   - pylammpsmpi >=0.0.9
-  - pyscal
+  - pyscal3
   - matplotlib
   - tqdm
   - uncertainties

environment-nolammps.yml

@@ -12,7 +12,6 @@ dependencies:
   - mendeleev
   - openmpi 
   - mpi4py
-  - pyscal
   - matplotlib
   - tqdm
   - uncertainties  

environment.yml

@@ -11,7 +11,6 @@ dependencies:
   - numpy
   - mpi4py =3.1.4
   - pylammpsmpi =0.2.3
-  - pyscal
   - matplotlib
   - tqdm
   - uncertainties

setup.py

@@ -43,7 +43,7 @@
     description="free energy calculation for python",
     install_requires=['matplotlib', 'pytest',
     'pyyaml', 'mendeleev', 
-    'tqdm', 'scipy', 'pydantic', 'pyscal', 'pyscal3'],
+    'tqdm', 'scipy', 'pydantic', 'pyscal3'],
     license="GNU General Public License v3",
     long_description=readme,
     long_description_content_type='text/markdown',

tests/input.yaml

@@ -3,10 +3,9 @@ calculations:
   lattice: FCC
   lattice_constant: 0.0
   mass: 63.546
+  #equilibration_control: berendsen
   md:
-    barostat_damping: 0.1
     n_small_steps: 1000
-    thermostat_damping: 0.1
     timestep: 0.001
   mode: ts
   n_equilibration_steps: 1000