calphy 1.2.14__py3-none-any.whl → 1.3.0__py3-none-any.whl

calphy/liquid.py

@@ -25,8 +25,6 @@ import numpy as np
 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
 from calphy.errors import *
@@ -115,11 +113,14 @@ class Liquid(cph.Phase):
         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)
 
         #Melt regime for the liquid
         lmp.velocity("all create", self.calc._temperature_high, np.random.randint(1, 10000))
@@ -177,6 +178,9 @@ class Liquid(cph.Phase):
         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")
@@ -184,7 +188,8 @@ class Liquid(cph.Phase):
 
         #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)
 
         #remap the box to get the correct pressure
         lmp = ph.remap_box(lmp, self.lx, self.ly, self.lz)
@@ -326,7 +331,8 @@ class Liquid(cph.Phase):
             self.rho, 50, 1.5)
 
         #Get ideal gas fe
-        f2 = get_ideal_gas_fe(self.calc._temperature, self.rho, 
+        f2 = get_ideal_gas_fe(self.calc._temperature, 
+            self.rho, 
             self.natoms, 
             [val['mass'] for key, val in self.calc._element_dict.items()], 
             [val['composition'] for key, val in self.calc._element_dict.items()])

calphy/phase.py

@@ -29,9 +29,8 @@ import numpy as np
 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
 from calphy.errors import *
 
@@ -57,11 +56,6 @@ class Phase:
         logfile = os.path.join(self.simfolder, "calphy.log")
         self.logger = ph.prepare_log(logfile, screen=log_to_screen)
 
-        self.logger.info("---------------input file----------------")
-        self.logger.info("commented out as causes crash when we're expanding the T range after a fail run")
-       # self.logger.info(yaml.safe_dump(self.calc.to_dict()))
-        self.logger.info("------------end of input file------------")
-
         if self.calc._pressure is None:
             pressure_string = "None"
         else:
@@ -134,9 +128,6 @@ class Phase:
         self.l = self.calc.lattice
         self.alat = self.calc.lattice_constant
         self.vol = None
-        #self.concentration = self.calc._composition
-        #self.dumpfile = False
-        self.prepare_lattice()
 
         #other properties
         self.cores = self.calc.queue.cores
@@ -196,39 +187,6 @@ class Phase:
                 self._from_dict(org_dict[key], val)
             else:
                 org_dict[key] = val        
-
-    def prepare_lattice(self):
-        """
-        Prepare the lattice for the simulation
-
-        Parameters
-        ----------
-        None
-
-        Returns
-        -------
-        None
-
-        Notes
-        -----
-        Calculates the lattic, lattice constant, number of atoms per unit cell
-        and concentration of the input system.
-        """
-        #l, alat, apc, conc, dumpfile = pl.prepare_lattice(self.calc)
-        #self.l = l
-        #self.alat = alat
-        #self.apc = apc
-        #self.concentration = self.calc.composition
-        #self.dumpfile = dumpfile
-        #self.logger.info("Lattice: %s with a=%f"%(self.l, self.alat))
-        #self.logger.info("%d atoms in the unit cell"%self.apc)
-        #self.logger.info("concentration:")
-        #self.logger.info(self.concentration)
-        #if self.l == "file":
-        #    if self.dumpfile:
-        #        self.logger.info("Input structure is read in from a LAMMPS dump file")
-        #    else:
-        #        self.logger.info("Input structure is read in from a LAMMPS data file")
                 
     def dump_current_snapshot(self, lmp, filename):
         """
@@ -669,35 +627,6 @@ class Phase:
         lmp.command("unfix            1")
         lmp.command("unfix            2")
 
-    def process_traj(self, filename, outfilename):
-        """
-        Process the out trajectory after averaging cycle and 
-        extract a configuration to run integration
-
-        Will be phased out...
-
-        Parameters
-        ----------
-        None
-
-        Returns
-        -------
-        None
-        
-        """
-        trajfile = os.path.join(self.simfolder, filename)
-        files = ptp.split_trajectory(trajfile)
-        conf = os.path.join(self.simfolder, outfilename)
-
-        ph.reset_timestep(conf, os.path.join(self.simfolder, "current.data"), 
-            init_commands=self.calc.md.init_commands,
-            script_mode=self.calc.script_mode)
-
-        os.remove(trajfile)
-        for file in files:
-            os.remove(file)
-
-
     def submit_report(self, extra_dict=None):
         """
         Submit final report containing results
@@ -794,13 +723,16 @@ class Phase:
         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)
 
         #remap the box to get the correct pressure
         lmp = ph.remap_box(lmp, self.lx, self.ly, self.lz)
@@ -889,7 +821,7 @@ class Phase:
             else:
                 self.check_if_solidfied(lmp, "traj.temp.dat")
 
-        lmp = ph.set_potential(lmp, self.calc, ghost_elements=self.calc._ghost_element_count)
+        lmp = ph.set_potential(lmp, self.calc)
 
         #reverse scaling
         lmp.command("variable         flambda equal ramp(${li},${lf})")
@@ -982,13 +914,16 @@ class Phase:
         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)
 
         #remap the box to get the correct pressure
         lmp = ph.remap_box(lmp, self.lx, self.ly, self.lz)
@@ -1071,13 +1006,16 @@ class Phase:
         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)
 
         #remap the box to get the correct pressure
         lmp = ph.remap_box(lmp, self.lx, self.ly, self.lz)

calphy/routines.py

@@ -443,6 +443,11 @@ def routine_composition_scaling(job):
     job.logger.info("Update pair coefficients")
     job.logger.info(f"pair coeff 1: {job.calc.pair_coeff[0]}")
     job.logger.info(f"pair coeff 2: {job.calc.pair_coeff[1]}")
+    job.calc._pair_style_names.append(job.calc._pair_style_names[0])
+    job.logger.info("Update pair styles")
+    job.logger.info(f"pair style 1: {job.calc._pair_style_names[0]}")
+    job.logger.info(f"pair style 2: {job.calc._pair_style_names[1]}")
+
     backup_element = job.calc.element.copy()
     job.calc.element = comp.pair_list_old
     #job.calc._ghost_element_count = len(comp.new_atomtype) - len()

calphy/solid.py

@@ -26,9 +26,7 @@ import yaml
 import copy
 import sys
 
-import pyscal.traj_process as ptp
 from calphy.integrators import *
-import calphy.lattice as pl
 import calphy.helpers as ph
 import calphy.phase as cph
 from calphy.errors import *
@@ -111,9 +109,13 @@ class Solid(cph.Phase):
         k_std = []
         for i in range(self.calc.n_elements):
             quant = np.loadtxt(file, usecols=(i+1, ), unpack=True)[-ncount+1:]
-            quant = 3*kb*self.calc._temperature/quant
-            k_mean.append(np.round(np.mean(quant), decimals=2))
-            k_std.append(np.round(np.std(quant), decimals=2))
+            mean_quant = np.round(np.mean(quant), decimals=2)
+            std_quant = np.round(np.std(quant), decimals=2)
+            if mean_quant == 0:
+                mean_quant = 1.00
+            mean_quant = 3*kb*self.calc._temperature/mean_quant
+            k_mean.append(mean_quant)
+            k_std.append(std_quant)
         return k_mean, k_std
         
 
@@ -213,14 +215,18 @@ class Solid(cph.Phase):
             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)
 
         #add some computes
         lmp.command("variable         mvol equal vol")
@@ -288,14 +294,19 @@ class Solid(cph.Phase):
             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)
+
 
         #add some computes
         lmp.command("variable         mvol equal vol")
@@ -364,16 +375,20 @@ class Solid(cph.Phase):
             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)
 
         #remap the box to get the correct pressure
         lmp = ph.remap_box(lmp, self.lx, self.ly, self.lz)
@@ -408,7 +423,7 @@ class Solid(cph.Phase):
         lmp.command("variable          step    equal step")
         lmp.command("variable          dU1      equal pe/atoms")
         for i in range(self.calc.n_elements):
-            lmp.command("variable          dU%d      equal f_ff%d/v_count%d"%(i+2, i+1, i+1))
+            lmp.command("variable          dU%d      equal f_ff%d"%(i+2, i+1))
         
         lmp.command("variable          lambda  equal f_ff1[1]")
 
@@ -432,6 +447,7 @@ class Solid(cph.Phase):
         str2 = []
         for i in range(self.calc.n_elements):
             str2.append("${dU%d}"%(i+2))
+
         str2.append("${lambda}\"")
         str2 = " ".join(str2)
         str3 = " screen no file forward_%d.dat"%iteration
@@ -457,6 +473,7 @@ class Solid(cph.Phase):
         str2 = []
         for i in range(self.calc.n_elements):
             str2.append("${dU%d}"%(i+2))
+
         str2.append("${lambda}\"")
         str2 = " ".join(str2)
         str3 = " screen no file backward_%d.dat"%iteration
@@ -499,13 +516,15 @@ class Solid(cph.Phase):
         Calculates the final work, energy dissipation and free energy by
         matching with Einstein crystal
         """
-        f1 = get_einstein_crystal_fe(self.calc._temperature, 
-            self.natoms, [val['mass'] for key, val in self.calc._element_dict.items()], 
-            self.vol, self.k, [val['composition'] for key, val in self.calc._element_dict.items()])
+        f1 = get_einstein_crystal_fe(
+            self.calc,  
+            self.vol, 
+            self.k)
+        
         w, q, qerr = find_w(self.simfolder, 
-            nelements=self.calc.n_elements, 
-            concentration=[val['composition'] for key, val in self.calc._element_dict.items()], nsims=self.calc.n_iterations, 
-            full=True, solid=True)
+            self.calc,
+            full=True, 
+            solid=True)
         
         self.fref = f1
         self.w = w

{calphy-1.2.14.dist-info → calphy-1.3.0.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: calphy
-Version: 1.2.14
+Version: 1.3.0
 Summary: free energy calculation for python
 Home-page: https://github.com/ICAMS/calphy
 Author: Sarath Menon, Yury Lysogorskiy, Ralf Drautz
@@ -21,7 +21,6 @@ Requires-Dist: mendeleev
 Requires-Dist: tqdm
 Requires-Dist: scipy
 Requires-Dist: pydantic
-Requires-Dist: pyscal
 Requires-Dist: pyscal3
 
 # calphy

calphy-1.3.0.dist-info/RECORD

@@ -0,0 +1,23 @@
+calphy/__init__.py,sha256=HnR9XnREXYsTl2lUvRlWplP3iug3Ng_h6Fl7UUAoQXI,233
+calphy/alchemy.py,sha256=MzmeNYz8zDi1ZDsrOErm5gmI5assQvzZwb_sIS3f30I,13257
+calphy/clitools.py,sha256=oDqaw0s-LJ7tAdW_Njk2SFljVx6K34Rs8sdMz48SNSI,4125
+calphy/composition_transformation.py,sha256=Hh240-iVGC8ATlJ3nQK757qVZIBrE2aw7dsF46mi3oo,15353
+calphy/errors.py,sha256=KN47RWTLbg1H_NZMrhCiJCbqjqJScJ1pgQAuzj1-l84,1268
+calphy/helpers.py,sha256=5P2JChRrJ6u5qHvyybGQ8eOumJIHk5no7IreYbg87YM,8244
+calphy/input.py,sha256=DgRSMuLKE5W8DLYg-4O8vuI7TYILA9ByJH1mHF3Q_h8,28774
+calphy/integrators.py,sha256=6r3CrdSep6pTYcUQCtO1_t9ab6U1YMLnHHmMau4NAT0,20709
+calphy/kernel.py,sha256=rd_-EfCiBhQjkxcVaoLtVJB2_qDgS-g-dQ0BZBTJQ_A,6190
+calphy/liquid.py,sha256=SAw7WXMEvWx0Ox02u8RAVxccj6e96Bt8G_vVDTNLDcU,13502
+calphy/phase.py,sha256=PkqG1mFHuXlP2zAeemENQWitAU9nV08GkxpoeH2Ihv0,44147
+calphy/phase_diagram.py,sha256=qXB3E0v3HDDpujPXjhFbx7X_xLpTGQYoWIGXdC_0NA8,10242
+calphy/queuekernel.py,sha256=4GMIYnjMiAPipoLNKP5noYcfeEOI_vCqm84zgokk7Xw,5321
+calphy/routines.py,sha256=W6OZEPv6HEG11EYsoIbum2WVrO3Ly36i5UWsYQ4oBdQ,17473
+calphy/scheduler.py,sha256=TS6aOjp2JpudVWTOIEjptqeDfgruWLwUQ_JVvuUCUgg,8532
+calphy/solid.py,sha256=49gT0wNOP3h8lRDXarULP-bU09lIrnDCTUcyxE7X-UE,19795
+calphy/splines.py,sha256=BGwUVz_qXQxUzpUCuZo6CsELcd5JVNWzI-Ttcz22G_E,61627
+calphy-1.3.0.dist-info/LICENSE,sha256=XIHGB5RZLIhOjjoO1bPf0II-qDbjhP5Cv5HJMRE9v1g,16651
+calphy-1.3.0.dist-info/METADATA,sha256=xJFRd275-y4a4XVzPLuJXuvFnSV4xUh68_s7ncmOpn4,4215
+calphy-1.3.0.dist-info/WHEEL,sha256=oiQVh_5PnQM0E3gPdiz09WCNmwiHDMaGer_elqB3coM,92
+calphy-1.3.0.dist-info/entry_points.txt,sha256=W9qq254koyWnAgo1jtfQP9bO5Q7sgZrzc8BMnfo3vf4,386
+calphy-1.3.0.dist-info/top_level.txt,sha256=w871dhMqPwgjjbifBWdkT9_aOnK1ek4Odrh8UnSG3PE,7
+calphy-1.3.0.dist-info/RECORD,,