Merge pull request #163 from ICAMS/update_pressure_convergence

Update pressure convergence

.bumpversion.cfg

@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 1.3.12
+current_version = 1.3.13
 commit = True
 tag = True
 

.github/workflows/testing.yml

@@ -14,33 +14,16 @@ jobs:
       matrix:
         include:
           - operating-system: ubuntu-latest
-            python-version: 3.9
-            label: linux-64-py-3-9
-            prefix: /usr/share/miniconda3/envs/my-env
+            python-version: 3.11
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v4
     - name: Setup Mambaforge
-      uses: conda-incubator/setup-miniconda@v2
+      uses: conda-incubator/setup-miniconda@v3
       with:
           python-version: ${{ matrix.python-version }}
-          miniforge-variant: Mambaforge
+          miniforge-version: latest
           channels: conda-forge
-          channel-priority: strict
-          activate-environment: my-env
-          use-mamba: true
-    - name: Set cache date and number
-      run: |
-          echo "DATE=$(date +'%Y%m%d')" >> $GITHUB_ENV
-          cat .github/variables/cache_number.env >> $GITHUB_ENV
-    - uses: actions/cache@v2
-      with:
-          path: ${{ matrix.prefix }}
-          key: ${{ matrix.label }}-conda-${{ hashFiles('environment.yml') }}-${{ env.DATE }}-${{ env.CACHE_NUMBER }}
-      id: cache
-    - name: Update environment
-      run: mamba env update -n my-env -f environment.yml
-      if: steps.cache.outputs.cache-hit != 'true'
-
+          environment-file: environment.yml   
     - name: run tests
       shell: bash -l {0}
       run: |

calphy/__init__.py

@@ -4,7 +4,7 @@
 from calphy.alchemy import Alchemy
 from calphy.routines import MeltingTemp
 
-__version__ = "1.3.12"
+__version__ = "1.3.13"
 
 def addtest(a,b):
     return a+b

calphy/input.py

@@ -40,7 +40,7 @@
 from ase.io import read, write
 import shutil
 
-__version__ = "1.3.12"
+__version__ = "1.3.13"
 
 def _check_equal(val):
     if not (val[0]==val[1]==val[2]):

calphy/phase.py

@@ -598,8 +598,12 @@ def process_pressure(self,):
 
         #now we can check if it converted
         file = os.path.join(self.simfolder, "avg.dat")
-        lx, ly, lz, ipress = np.loadtxt(file, usecols=(1, 2, 3, 4), unpack=True)
-        lxpc = ipress
+        #we have to clean the data, so as just the last block is selected
+        lx, ly, lz, lxpc = np.loadtxt(file, usecols=(1, 2, 3, 4), unpack=True)
+        lx = lx[-ncount+1:]
+        ly = ly[-ncount+1:]
+        lz = lx[-ncount+1:]
+        lxpc = lxpc[-ncount+1:]
         mean = np.mean(lxpc)
         std = np.std(lxpc)
         volatom = np.mean((lx*ly*lz)/self.natoms)
@@ -612,16 +616,20 @@ def finalise_pressure(self,):
             ncount = int(self.calc.md.n_small_steps)//int(self.calc.md.n_every_steps*self.calc.md.n_repeat_steps)
 
         file = os.path.join(self.simfolder, "avg.dat")
-        lx, ly, lz, ipress = np.loadtxt(file, usecols=(1, 2, 3, 4), unpack=True)        
-        lxpc = ipress
+        lx, ly, lz, lxpc = np.loadtxt(file, usecols=(1, 2, 3, 4), unpack=True)        
+        lx = lx[-ncount+1:]
+        ly = ly[-ncount+1:]
+        lz = lx[-ncount+1:]
+        lxpc = lxpc[-ncount+1:]
+
         mean = np.mean(lxpc)
         std = np.std(lxpc)
         volatom = np.mean((lx*ly*lz)/self.natoms)
 
         self.calc._pressure = mean
-        self.lx = np.round(np.mean(lx[-ncount+1:]), decimals=3)
-        self.ly = np.round(np.mean(ly[-ncount+1:]), decimals=3)
-        self.lz = np.round(np.mean(lz[-ncount+1:]), decimals=3)
+        self.lx = np.round(np.mean(lx), decimals=3)
+        self.ly = np.round(np.mean(ly), decimals=3)
+        self.lz = np.round(np.mean(lz), decimals=3)
         self.volatom = volatom
         self.vol = self.lx*self.ly*self.lz
         self.rho = self.natoms/(self.lx*self.ly*self.lz)

setup.py

@@ -53,7 +53,7 @@
     packages=find_packages(include=['calphy', 'calphy.*']),
     test_suite='tests',
     url='https://github.com/ICAMS/calphy',
-    version='1.3.12',
+    version='1.3.13',
     zip_safe=False,
     entry_points={
         'console_scripts': [