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Fix order #106

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merged 8 commits into from
Feb 17, 2024
Merged

Fix order #106

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7d55b89
fx pair styles
srmnitc Feb 16, 2024
86e2914
fix phase
srmnitc Feb 16, 2024
c5f70b3
fix solid
srmnitc Feb 16, 2024
d0d192b
fix liquid
srmnitc Feb 16, 2024
a6159f1
fix alchemy
srmnitc Feb 16, 2024
0ec186c
add mass command
srmnitc Feb 16, 2024
45411cc
add mass command
srmnitc Feb 16, 2024
880e651
update itignore
srmnitc Feb 16, 2024
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5 changes: 5 additions & 0 deletions .gitignore
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Original file line number Diff line number Diff line change
Expand Up @@ -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
Expand Up @@ -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")
Expand Down Expand Up @@ -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")
Expand All @@ -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
Expand Down
11 changes: 9 additions & 2 deletions calphy/liquid.py
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Original file line number Diff line number Diff line change
Expand Up @@ -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))
Expand Down Expand Up @@ -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)
Expand Down
15 changes: 12 additions & 3 deletions calphy/phase.py
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Original file line number Diff line number Diff line change
Expand Up @@ -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)
Expand Down Expand Up @@ -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)
Expand Down Expand Up @@ -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)
Expand Down
25 changes: 19 additions & 6 deletions calphy/solid.py
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Original file line number Diff line number Diff line change
Expand Up @@ -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")
Expand Down Expand Up @@ -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")
Expand Down Expand Up @@ -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)
Expand Down
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