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Merge pull request #106 from ICAMS/fix_order
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Fix order
@srmnitc
srmnitc authored Feb 17, 2024

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driesvints Dries Vints
GPG key ID: BDD2ED2E8C8025E7
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2 parents d8c50b6 + 880e651 commit 564d2bc
Showing 5 changed files with 54 additions and 13 deletions.
5 changes: 5 additions & 0 deletions .gitignore
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Original file line number Diff line number Diff line change
@@ -18,3 +18,8 @@ tscale-*
pscale-*
alchemy-*
*.npy
*.data
*.dump
mts-*
melting_temperature-*
composition_scaling-*
11 changes: 9 additions & 2 deletions calphy/alchemy.py
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Original file line number Diff line number Diff line change
@@ -77,11 +77,14 @@ def run_averaging(self):
lmp = ph.create_object(self.cores, self.simfolder, self.calc.md.timestep,
self.calc.md.cmdargs, self.calc.md.init_commands)

lmp.command(f'pair_style {self.calc._pair_style_with_options[0]}')

#set up structure
lmp = ph.create_structure(lmp, self.calc)

#set up potential
lmp = ph.set_potential(lmp, self.calc, ghost_elements=self.calc._ghost_element_count)
lmp.command(f'pair_coeff {self.calc.pair_coeff[0]}')
lmp = ph.set_mass(lmp, self.calc, ghost_elements=self.calc._ghost_element_count)

#add some computes
lmp.command("variable mvol equal vol")
@@ -143,6 +146,8 @@ def run_integration(self, iteration=1):
# Adiabatic switching parameters.
lmp.command("variable li equal 1.0")
lmp.command("variable lf equal 0.0")

lmp.command(f'pair_style {self.calc._pair_style_with_options[0]}')

#read dump file
#conf = os.path.join(self.simfolder, "conf.equilibration.dump")
@@ -151,7 +156,9 @@ def run_integration(self, iteration=1):

#set up hybrid potential
#here we only need to set one potential
lmp = ph.set_potential(lmp, self.calc, ghost_elements=self.calc._ghost_element_count)
lmp.command(f'pair_coeff {self.calc.pair_coeff[0]}')
lmp = ph.set_mass(lmp, self.calc, ghost_elements=self.calc._ghost_element_count)

#lmp = ph.set_double_hybrid_potential(lmp, self.options, self.calc._pressureair_style, self.calc._pressureair_coeff)

#remap the box to get the correct pressure
11 changes: 9 additions & 2 deletions calphy/liquid.py
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Original file line number Diff line number Diff line change
@@ -113,11 +113,14 @@ def run_averaging(self):
lmp = ph.create_object(self.cores, self.simfolder, self.calc.md.timestep,
self.calc.md.cmdargs, self.calc.md.init_commands)

lmp.command(f'pair_style {self.calc._pair_style_with_options[0]}')

#set up structure
lmp = ph.create_structure(lmp, self.calc)

#set up potential
lmp = ph.set_potential(lmp, self.calc, ghost_elements=self.calc._ghost_element_count)
lmp.command(f'pair_coeff {self.calc.pair_coeff[0]}')
lmp = ph.set_mass(lmp, self.calc, ghost_elements=self.calc._ghost_element_count)

#Melt regime for the liquid
lmp.velocity("all create", self.calc._temperature_high, np.random.randint(1, 10000))
@@ -175,14 +178,18 @@ def run_integration(self, iteration=1):
lmp.command("variable li equal 1.0")
lmp.command("variable lf equal 0.0")


lmp.command(f'pair_style {self.calc._pair_style_with_options[0]}')

#read in the conf file
#conf = os.path.join(self.simfolder, "conf.equilibration.dump")
conf = os.path.join(self.simfolder, "conf.equilibration.data")
lmp = ph.read_data(lmp, conf)

#set hybrid ufm and normal potential
#lmp = ph.set_hybrid_potential(lmp, self.options, self.eps)
lmp = ph.set_potential(lmp, self.calc, ghost_elements=self.calc._ghost_element_count)
lmp.command(f'pair_coeff {self.calc.pair_coeff[0]}')
lmp = ph.set_mass(lmp, self.calc, ghost_elements=self.calc._ghost_element_count)

#remap the box to get the correct pressure
lmp = ph.remap_box(lmp, self.lx, self.ly, self.lz)
15 changes: 12 additions & 3 deletions calphy/phase.py
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Original file line number Diff line number Diff line change
@@ -728,13 +728,16 @@ def reversible_scaling(self, iteration=1):
lmp.command("variable li equal %f"%li)
lmp.command("variable lf equal %f"%lf)

lmp.command(f'pair_style {self.calc._pair_style_with_options[0]}')

#read in conf file
#conf = os.path.join(self.simfolder, "conf.equilibration.dump")
conf = os.path.join(self.simfolder, "conf.equilibration.data")
lmp = ph.read_data(lmp, conf)

#set up potential
lmp = ph.set_potential(lmp, self.calc, ghost_elements=self.calc._ghost_element_count)
lmp.command(f'pair_coeff {self.calc.pair_coeff[0]}')
lmp = ph.set_mass(lmp, self.calc, ghost_elements=self.calc._ghost_element_count)

#remap the box to get the correct pressure
lmp = ph.remap_box(lmp, self.lx, self.ly, self.lz)
@@ -916,13 +919,16 @@ def temperature_scaling(self, iteration=1):
lmp.command("variable li equal %f"%li)
lmp.command("variable lf equal %f"%lf)

lmp.command(f'pair_style {self.calc._pair_style_with_options[0]}')

#read in conf
#conf = os.path.join(self.simfolder, "conf.equilibration.dump")
conf = os.path.join(self.simfolder, "conf.equilibration.data")
lmp = ph.read_data(lmp, conf)

#set up potential
lmp = ph.set_potential(lmp, self.calc, ghost_elements=self.calc._ghost_element_count)
lmp.command(f'pair_coeff {self.calc.pair_coeff[0]}')
lmp = ph.set_mass(lmp, self.calc, ghost_elements=self.calc._ghost_element_count)

#remap the box to get the correct pressure
lmp = ph.remap_box(lmp, self.lx, self.ly, self.lz)
@@ -1005,13 +1011,16 @@ def pressure_scaling(self, iteration=1):
lmp.command("variable p0 equal %f"%p0)
lmp.command("variable pf equal %f"%pf)

lmp.command(f'pair_style {self.calc._pair_style_with_options[0]}')

#read in conf
#conf = os.path.join(self.simfolder, "conf.dump")
conf = os.path.join(self.simfolder, "conf.equilibration.data")
lmp = ph.read_data(lmp, conf)

#set up potential
lmp = ph.set_potential(lmp, self.calc, ghost_elements=self.calc._ghost_element_count)
lmp.command(f'pair_coeff {self.calc.pair_coeff[0]}')
lmp = ph.set_mass(lmp, self.calc, ghost_elements=self.calc._ghost_element_count)

#remap the box to get the correct pressure
lmp = ph.remap_box(lmp, self.lx, self.ly, self.lz)
25 changes: 19 additions & 6 deletions calphy/solid.py
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Original file line number Diff line number Diff line change
@@ -211,14 +211,18 @@ def run_interactive_averaging(self):
init_commands=self.calc.md.init_commands,
script_mode=self.calc.script_mode)

#set up potential
if self.calc.potential_file is None:
lmp.command(f'pair_style {self.calc._pair_style_with_options[0]}')

#set up structure
lmp = ph.create_structure(lmp, self.calc)

#set up potential
if self.calc.potential_file is None:
lmp = ph.set_potential(lmp, self.calc, ghost_elements=self.calc._ghost_element_count)
lmp.command(f'pair_coeff {self.calc.pair_coeff[0]}')
else:
lmp.command("include %s"%self.calc.potential_file)
lmp = ph.set_mass(lmp, self.calc, ghost_elements=self.calc._ghost_element_count)

#add some computes
lmp.command("variable mvol equal vol")
@@ -286,14 +290,19 @@ def run_minimal_averaging(self):
init_commands=self.calc.md.init_commands,
script_mode=self.calc.script_mode)

#set up potential
if self.calc.potential_file is None:
lmp.command(f'pair_style {self.calc._pair_style_with_options[0]}')

#set up structure
lmp = ph.create_structure(lmp, self.calc, species=self.calc.n_elements+self.calc._ghost_element_count)

#set up potential
if self.calc.potential_file is None:
lmp = ph.set_potential(lmp, self.calc, ghost_elements=self.calc._ghost_element_count)
lmp.command(f'pair_coeff {self.calc.pair_coeff[0]}')
else:
lmp.command("include %s"%self.calc.potential_file)
lmp = ph.set_mass(lmp, self.calc, ghost_elements=self.calc._ghost_element_count)


#add some computes
lmp.command("variable mvol equal vol")
@@ -362,16 +371,20 @@ def run_integration(self, iteration=1):
init_commands=self.calc.md.init_commands,
script_mode=self.calc.script_mode)

#set up potential
if self.calc.potential_file is None:
lmp.command(f'pair_style {self.calc._pair_style_with_options[0]}')

#read in the conf file
#conf = os.path.join(self.simfolder, "conf.equilibration.dump")
conf = os.path.join(self.simfolder, "conf.equilibration.data")
lmp = ph.read_data(lmp, conf)

#set up potential
if self.calc.potential_file is None:
lmp = ph.set_potential(lmp, self.calc, ghost_elements=self.calc._ghost_element_count)
lmp.command(f'pair_coeff {self.calc.pair_coeff[0]}')
else:
lmp.command("include %s"%self.calc.potential_file)
lmp = ph.set_mass(lmp, self.calc, ghost_elements=self.calc._ghost_element_count)

#remap the box to get the correct pressure
lmp = ph.remap_box(lmp, self.lx, self.ly, self.lz)

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