From 63a4a2ad2d083e040b8f50af133b4b18bfc80f90 Mon Sep 17 00:00:00 2001 From: Sarath Menon Date: Mon, 11 Sep 2023 11:15:08 +0200 Subject: [PATCH] update for tri --- calphy/phase.py | 6 +++--- calphy/solid.py | 6 ++++++ notebooks/running_from_notebook.ipynb | 2 +- 3 files changed, 10 insertions(+), 4 deletions(-) diff --git a/calphy/phase.py b/calphy/phase.py index 6523cb0..bba9daf 100644 --- a/calphy/phase.py +++ b/calphy/phase.py @@ -483,7 +483,7 @@ def run_iterative_pressure_convergence(self, lmp): self.fix_berendsen(lmp) - lmp.command("fix 2 all ave/time %d %d %d v_mlx v_mly v_mlz v_mpress file avg.dat"%(int(self.calc.md.n_every_steps), + lmp.command("fix 2 all ave/time %d %d %d v_mlx v_mly v_mlz v_mpress v_mvol v_mxy v_mxz v_myz file avg.dat"%(int(self.calc.md.n_every_steps), int(self.calc.md.n_repeat_steps), int(self.calc.md.n_every_steps*self.calc.md.n_repeat_steps))) laststd = 0.00 @@ -555,9 +555,9 @@ def run_minimal_pressure_convergence(self, lmp): self.fix_berendsen(lmp) - lmp.command("fix 2 all ave/time %d %d %d v_mlx v_mly v_mlz v_mpress file avg.dat"%(int(self.calc.md.n_every_steps), + lmp.command("fix 2 all ave/time %d %d %d v_mlx v_mly v_mlz v_mpress v_mvol v_mxy v_mxz v_myz file avg.dat"%(int(self.calc.md.n_every_steps), int(self.calc.md.n_repeat_steps), int(self.calc.md.n_every_steps*self.calc.md.n_repeat_steps))) - + lmp.command("run %d"%int(self.calc.md.n_small_steps)) lmp.command("run %d"%int(self.calc.n_equilibration_steps)) diff --git a/calphy/solid.py b/calphy/solid.py index c2636bf..7f3f871 100644 --- a/calphy/solid.py +++ b/calphy/solid.py @@ -226,6 +226,9 @@ def run_interactive_averaging(self): lmp.command("variable mlx equal lx") lmp.command("variable mly equal ly") lmp.command("variable mlz equal lz") + lmp.command("variable mxy equal xy") + lmp.command("variable mxz equal xz") + lmp.command("variable myz equal yz") lmp.command("variable mpress equal press") #Run if a constrained lattice is not needed @@ -301,6 +304,9 @@ def run_minimal_averaging(self): lmp.command("variable mlx equal lx") lmp.command("variable mly equal ly") lmp.command("variable mlz equal lz") + lmp.command("variable mxy equal xy") + lmp.command("variable mxz equal xz") + lmp.command("variable myz equal yz") lmp.command("variable mpress equal press") #Run if a constrained lattice is not needed diff --git a/notebooks/running_from_notebook.ipynb b/notebooks/running_from_notebook.ipynb index dc2b186..5451a41 100644 --- a/notebooks/running_from_notebook.ipynb +++ b/notebooks/running_from_notebook.ipynb @@ -306,7 +306,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.10.9" + "version": "3.9.18" } }, "nbformat": 4,