calphy 1.4.5__py3-none-any.whl → 1.4.6__py3-none-any.whl

calphy/scheduler.py

@@ -3,14 +3,14 @@ calphy: a Python library and command line interface for automated free
 energy calculations.
 
 Copyright 2021  (c) Sarath Menon^1, Yury Lysogorskiy^2, Ralf Drautz^2
-^1: Max Planck Institut für Eisenforschung, Dusseldorf, Germany 
+^1: Max Planck Institut für Eisenforschung, Dusseldorf, Germany
 ^2: Ruhr-University Bochum, Bochum, Germany
 
-calphy is published and distributed under the Academic Software License v1.0 (ASL). 
-calphy is distributed in the hope that it will be useful for non-commercial academic research, 
-but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  
+calphy is published and distributed under the Academic Software License v1.0 (ASL).
+calphy is distributed in the hope that it will be useful for non-commercial academic research,
+but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
 calphy API is published and distributed under the BSD 3-Clause "New" or "Revised" License
-See the LICENSE FILE for more details. 
+See the LICENSE FILE for more details.
 
 More information about the program can be found in:
 Menon, Sarath, Yury Lysogorskiy, Jutta Rogal, and Ralf Drautz.
@@ -25,25 +25,26 @@ import subprocess as sub
 import os
 import stat
 
+
 class Local:
     """
     Local submission script
     """
+
     def __init__(self, options, cores=1, directory=os.getcwd()):
-        self.queueoptions = {"scheduler": "local",
-                             "jobname": "tis",
-                             "queuename": None,
-                             "memory": None,
-                             "cores": cores,
-                             "hint": None,
-                             "directory": directory,
-                             "options": [],
-                             "commands": [],
-                             "modules": [],
-                             "header": "#!/bin/bash"
-
-                            }
-        for (key, val) in options.items():
+        self.queueoptions = {
+            "scheduler": "local",
+            "jobname": "tis",
+            "queuename": None,
+            "memory": None,
+            "cores": cores,
+            "hint": None,
+            "directory": directory,
+            "options": [],
+            "commands": [],
+            "header": "#!/bin/bash",
+        }
+        for key, val in options.items():
             if key in self.queueoptions.keys():
                 if val is not None:
                     self.queueoptions[key] = val
@@ -60,14 +61,10 @@ class Local:
             fout.write(self.queueoptions["header"])
             fout.write("\n")
 
-            #now write modules
-            for module in self.queueoptions["modules"]:
-                fout.write("module load %s\n"   %module)
-
-            #now finally commands
+            # now finally commands
             for command in self.queueoptions["commands"]:
-                fout.write("%s\n"   %command)
-            fout.write("%s > %s 2> %s\n"   %(self.maincommand, jobout, joberr))
+                fout.write("%s\n" % command)
+            fout.write("%s > %s 2> %s\n" % (self.maincommand, jobout, joberr))
         self.script = outfile
 
     def submit(self):
@@ -77,41 +74,42 @@ class Local:
         st = os.stat(self.script)
         os.chmod(self.script, st.st_mode | stat.S_IEXEC)
         cmd = [self.script]
-        proc = sub.Popen(cmd, stdin=sub.PIPE,stdout=sub.PIPE,stderr=sub.PIPE)
+        proc = sub.Popen(cmd, stdin=sub.PIPE, stdout=sub.PIPE, stderr=sub.PIPE)
         return proc
 
+
 class SLURM:
     """
     Slurm class for writing submission script
     """
+
     def __init__(self, options, cores=1, directory=os.getcwd()):
         """
         Create class
         """
-        self.queueoptions = {"scheduler": "slurm",
-                             "jobname": "tis",
-                             "queuename": None,
-                             "walltime": "23:59:00",
-                             "memory": "3GB",
-                             "cores": cores,
-                             "hint": "nomultithread",
-                             "directory": directory,
-                             "options": [],
-                             "commands": [ "uss=$(whoami)",
-                                           "find /dev/shm/ -user $uss -type f -mmin +30 -delete",
-                                         ],
-                             "modules": [],
-                             "header": "#!/bin/bash"
-
-                            }
-        for (key, val) in options.items():
+        self.queueoptions = {
+            "scheduler": "slurm",
+            "jobname": "tis",
+            "queuename": None,
+            "walltime": "23:59:00",
+            "memory": "3GB",
+            "cores": cores,
+            "hint": "nomultithread",
+            "directory": directory,
+            "options": [],
+            "commands": [
+                "uss=$(whoami)",
+                "find /dev/shm/ -user $uss -type f -mmin +30 -delete",
+            ],
+            "header": "#!/bin/bash",
+        }
+        for key, val in options.items():
             if key in self.queueoptions.keys():
                 if val is not None:
                     if val != "":
                         self.queueoptions[key] = val
         self.maincommand = ""
 
-
     def write_script(self, outfile):
         """
         Write the script file
@@ -123,28 +121,24 @@ class SLURM:
             fout.write(self.queueoptions["header"])
             fout.write("\n")
 
-            #write the main header options
-            fout.write("#SBATCH --job-name=%s\n" %self.queueoptions["jobname"])
-            fout.write("#SBATCH --time=%s\n"     %self.queueoptions["walltime"])
+            # write the main header options
+            fout.write("#SBATCH --job-name=%s\n" % self.queueoptions["jobname"])
+            fout.write("#SBATCH --time=%s\n" % self.queueoptions["walltime"])
             if self.queueoptions["queuename"] is not None:
-                fout.write("#SBATCH --partition=%s\n"%self.queueoptions["queuename"])
-            fout.write("#SBATCH --ntasks=%s\n"   %str(self.queueoptions["cores"]))
-            fout.write("#SBATCH --mem-per-cpu=%s\n"%self.queueoptions["memory"])
-            fout.write("#SBATCH --hint=%s\n"     %self.queueoptions["hint"])
-            fout.write("#SBATCH --chdir=%s\n"    %self.queueoptions["directory"])
+                fout.write("#SBATCH --partition=%s\n" % self.queueoptions["queuename"])
+            fout.write("#SBATCH --ntasks=%s\n" % str(self.queueoptions["cores"]))
+            fout.write("#SBATCH --mem-per-cpu=%s\n" % self.queueoptions["memory"])
+            fout.write("#SBATCH --hint=%s\n" % self.queueoptions["hint"])
+            fout.write("#SBATCH --chdir=%s\n" % self.queueoptions["directory"])
 
-            #now write extra options
+            # now write extra options
             for option in self.queueoptions["options"]:
-                fout.write("#SBATCH %s\n"   %option)
+                fout.write("#SBATCH %s\n" % option)
 
-            #now write modules
-            for module in self.queueoptions["modules"]:
-                fout.write("module load %s\n"   %module)
-
-            #now finally commands
+            # now finally commands
             for command in self.queueoptions["commands"]:
-                fout.write("%s\n"   %command)
-            fout.write("%s > %s 2> %s\n"   %(self.maincommand, jobout, joberr))
+                fout.write("%s\n" % command)
+            fout.write("%s > %s 2> %s\n" % (self.maincommand, jobout, joberr))
 
         self.script = outfile
 
@@ -152,40 +146,41 @@ class SLURM:
         """
         Submit the job
         """
-        cmd = ['sbatch', self.script]
-        proc = sub.Popen(cmd, stdin=sub.PIPE,stdout=sub.PIPE,stderr=sub.PIPE)
+        cmd = ["sbatch", self.script]
+        proc = sub.Popen(cmd, stdin=sub.PIPE, stdout=sub.PIPE, stderr=sub.PIPE)
         print(f'submitting {self.queueoptions["jobname"]}')
         proc.communicate()
         return proc
 
 
-
 class SGE:
     """
     Slurm class for writing submission script
     """
+
     def __init__(self, options, cores=1, directory=os.getcwd()):
         """
         Create class
         """
-        self.queueoptions = {"scheduler": "sge",
-                             "jobname": "tis",
-                             "walltime": "23:59:00",
-                             "queuename": None,
-                             "memory": "3GB",
-                             "system": "smp",
-                             "commands": [],
-                             "modules": [], 
-                             "options": ["-j y",
-                                         "-R y",
-                                         "-P ams.p",
-                                        ],
-                             "cores": cores,
-                             "hint": None,
-                             "directory": directory,
-                             "header": "#!/bin/bash"
-                            }
-        for (key, val) in options.items():
+        self.queueoptions = {
+            "scheduler": "sge",
+            "jobname": "tis",
+            "walltime": "23:59:00",
+            "queuename": None,
+            "memory": "3GB",
+            "system": "smp",
+            "commands": [],
+            "options": [
+                "-j y",
+                "-R y",
+                "-P ams.p",
+            ],
+            "cores": cores,
+            "hint": None,
+            "directory": directory,
+            "header": "#!/bin/bash",
+        }
+        for key, val in options.items():
             if key in self.queueoptions.keys():
                 if val is not None:
                     self.queueoptions[key] = val
@@ -195,40 +190,40 @@ class SGE:
         """
         Write the script file
         """
+        jobout = ".".join([outfile, "out"])
+        joberr = ".".join([outfile, "err"])
+
         with open(outfile, "w") as fout:
             fout.write(self.queueoptions["header"])
             fout.write("\n")
 
-            #write the main header options
-            fout.write("#$ -N %s\n" %self.queueoptions["jobname"])
-            fout.write("#$ -l h_rt=%s\n"     %self.queueoptions["walltime"])
-            fout.write("#$ -l qname=%s\n"%self.queueoptions["queuename"])
-            fout.write("#$ -pe %s %s\n"   %( self.queueoptions["system"], str(self.queueoptions["cores"])))
-            fout.write("#$ -l h_vmem=%s\n"%self.queueoptions["memory"])
-            fout.write("#$ -cwd %s\n"    %self.queueoptions["directory"])
-
-            #now write extra options
+            # write the main header options
+            fout.write("#$ -N %s\n" % self.queueoptions["jobname"])
+            fout.write("#$ -l h_rt=%s\n" % self.queueoptions["walltime"])
+            fout.write("#$ -l qname=%s\n" % self.queueoptions["queuename"])
+            fout.write(
+                "#$ -pe %s %s\n"
+                % (self.queueoptions["system"], str(self.queueoptions["cores"]))
+            )
+            fout.write("#$ -l h_vmem=%s\n" % self.queueoptions["memory"])
+            fout.write("#$ -cwd %s\n" % self.queueoptions["directory"])
+
+            # now write extra options
             for option in self.queueoptions["options"]:
-                fout.write("#$ %s\n"   %option)
-
-            #now write modules
-            for module in self.queueoptions["modules"]:
-                fout.write("module load %s\n"   %module)
+                fout.write("#$ %s\n" % option)
 
-            #now finally commands
+            # now finally commands
             for command in self.queueoptions["commands"]:
-                fout.write("%s\n"   %command)
+                fout.write("%s\n" % command)
 
-            fout.write("%s > %s 2> %s\n"   %(self.maincommand, jobout, joberr))
-        
-        self.script = outfile   
+            fout.write("%s > %s 2> %s\n" % (self.maincommand, jobout, joberr))
 
+        self.script = outfile
 
     def submit(self):
         """
         Submit the job
         """
-        cmd = ['qsub', self.script]
-        proc = sub.Popen(cmd, stdin=sub.PIPE,stdout=sub.PIPE,stderr=sub.PIPE)
+        cmd = ["qsub", self.script]
+        proc = sub.Popen(cmd, stdin=sub.PIPE, stdout=sub.PIPE, stderr=sub.PIPE)
         return proc
-    

{calphy-1.4.5.dist-info → calphy-1.4.6.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: calphy
-Version: 1.4.5
+Version: 1.4.6
 Summary: free energy calculation for python
 Home-page: https://github.com/ICAMS/calphy
 Author: Sarath Menon, Yury Lysogorskiy, Ralf Drautz

{calphy-1.4.5.dist-info → calphy-1.4.6.dist-info}/RECORD

@@ -1,25 +1,25 @@
-calphy/__init__.py,sha256=ajDpPU1OkfwLqHSjYro8IgKKujLpCZhkszpGfQHA_5U,233
+calphy/__init__.py,sha256=K3G6Hr3pdNGqjHH0ZvD0OGh4ukLTKdlkcm_JLSyCKw8,233
 calphy/alchemy.py,sha256=IEYLfsJRsjfB0zFfApmxGbYXif7IE6mUY_vjTZoXdII,17236
 calphy/clitools.py,sha256=ZUr6ZfdopFxWMbrzNT_TQaUA16iPmZ3144oPcwcDazY,4433
-calphy/composition_transformation.py,sha256=z3X4fFVoym6QgRDpLBYZ_fM9V0IgJvBq-wITu1nwVmw,17247
+calphy/composition_transformation.py,sha256=S-4H4UDjy_1Ucn6qgAoMaCsDRfNc8zJ5DH4_BqOGAT4,19336
 calphy/errors.py,sha256=KN47RWTLbg1H_NZMrhCiJCbqjqJScJ1pgQAuzj1-l84,1268
-calphy/helpers.py,sha256=goN_n5kceSaevjBilQDgHD5-QZxsQsOwTiWsY00jMcM,8411
-calphy/input.py,sha256=3xVoJcbwq3T7y_1drIvg1Erel9dz6y9A4rgNsncEfgw,36225
+calphy/helpers.py,sha256=oPDlnXKoOLP1uwnilDgorKs_FlvunN1-bwChEwDslDE,8608
+calphy/input.py,sha256=gITbf-X-pdPm7pAd8CMOFV6rd4MaiNJFKLOqfG0TfWA,39578
 calphy/integrators.py,sha256=q5sIJX3nh4c9kmDQJ4Pqhvm38tRWKELoJwm5gW0lqws,21858
 calphy/kernel.py,sha256=wjSpQ59PN-aqHQ1kvOxTYnP2d3wE1Zx4A9ZhqQFqGlI,6311
 calphy/liquid.py,sha256=ECF3DxPZv7XHnmQzk_yz1fol-Vsd98lRojTMAR1YS3M,15025
 calphy/phase.py,sha256=F4GRrEG0IDR6f0rFabQYP7aYBzpKAyxPvol-n7vAj08,53540
-calphy/phase_diagram.py,sha256=Yu192y7bhWsj-xQL7ITSBdMHKXJ6I_4gV0cLfdXTOa4,27791
+calphy/phase_diagram.py,sha256=85ZTzyQX_a902wqRJ49MQsQEHZiZAwfHOaruskVhlD4,32417
 calphy/postprocessing.py,sha256=XxpFGbR8dUoKhGb7GCPEWPA4CWl7ZftuM1cN4tz7-fQ,15164
 calphy/queuekernel.py,sha256=4GMIYnjMiAPipoLNKP5noYcfeEOI_vCqm84zgokk7Xw,5321
 calphy/routines.py,sha256=YaVoAbeAbZ3ytAP_A0o5ngkpPiXpc_lk2I0bN3nqhPs,17858
-calphy/scheduler.py,sha256=nIxlKKGj8ol_FuYMMtXrQinPGhPlYs2h-JsEGHC7_wY,8666
+calphy/scheduler.py,sha256=U-FQttOHOUiL-qR9gepvdGn1fxbfhZhHezuWdO3Fgyk,7575
 calphy/solid.py,sha256=zHSqri8roW23hIQ21huxHHJqq3P5EklSj6Z0z9ywfbc,21911
 calphy/splines.py,sha256=BGwUVz_qXQxUzpUCuZo6CsELcd5JVNWzI-Ttcz22G_E,61627
 calphy/utils.py,sha256=0UpsYoxjS5N-iGs-cdm0YDMkLF8IHvKO3smXDHrj3eg,3818
-calphy-1.4.5.dist-info/licenses/LICENSE,sha256=XIHGB5RZLIhOjjoO1bPf0II-qDbjhP5Cv5HJMRE9v1g,16651
-calphy-1.4.5.dist-info/METADATA,sha256=za1qlwUMSyzxwl2bghD8i9HdGRMLKpxslgpkX-jiM2s,4469
-calphy-1.4.5.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
-calphy-1.4.5.dist-info/entry_points.txt,sha256=KX5dP2iYy9GB4Mo0lbCPAz6jo-8b1Gt9GDmsDFzt9pQ,439
-calphy-1.4.5.dist-info/top_level.txt,sha256=w871dhMqPwgjjbifBWdkT9_aOnK1ek4Odrh8UnSG3PE,7
-calphy-1.4.5.dist-info/RECORD,,
+calphy-1.4.6.dist-info/licenses/LICENSE,sha256=XIHGB5RZLIhOjjoO1bPf0II-qDbjhP5Cv5HJMRE9v1g,16651
+calphy-1.4.6.dist-info/METADATA,sha256=4gAFxTRF2NTh1I_3Z5zYnotK_Fvdc9PaWPWp2_qotHY,4469
+calphy-1.4.6.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
+calphy-1.4.6.dist-info/entry_points.txt,sha256=KX5dP2iYy9GB4Mo0lbCPAz6jo-8b1Gt9GDmsDFzt9pQ,439
+calphy-1.4.6.dist-info/top_level.txt,sha256=w871dhMqPwgjjbifBWdkT9_aOnK1ek4Odrh8UnSG3PE,7
+calphy-1.4.6.dist-info/RECORD,,