refactored for current millenium

PySCeS · Aug 24, 2020 · 2344f52 · 2344f52
1 parent c005e26
commit 2344f52
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Showing 6 changed files with 190 additions and 107 deletions.
diff --git a/pysces/PyscesModel.py b/pysces/PyscesModel.py
@@ -2108,7 +2108,6 @@ def Stoichiometry_Load_Serial(self):
         stc = self.SerialDecode(self.ModelFile[:-4] + '_stoichiometry')
         return stc
 
-    # new powerslave method - brett 20050825
     def Stoichiometry_Analyse(self, override=0, load=0):
         """
         Stoichiometry_Analyse(override=0,load=0)

diff --git a/pysces/PyscesParScan.py b/pysces/PyscesParScan.py
@@ -125,7 +125,7 @@ def genScanSpace(self):
         spr = self.scans_per_run
         Tsteps = 1
         for gen in self.GenOrder:
-            if self.GenDict[gen][4] == False:  # don't increase Tsteps for slaves
+            if self.GenDict[gen][4] == False:  # don't increase Tsteps for followers
                 Tsteps *= self.GenDict[gen][2]
         for step in range(Tsteps):
             pars = self.__nextValue__()

diff --git a/pysces/PyscesScan.py b/pysces/PyscesScan.py
@@ -118,7 +118,7 @@ def addUserOutput(self, *kw):
         print('MaxMode', MaxMode)
         self.UserOutputList = output
 
-    def addScanParameter(self, name, start, end, points, log=False, slave=False):
+    def addScanParameter(self, name, start, end, points, log=False, follower=False):
         """
         Add a parameter to scan (an axis if you like) input is:
 
@@ -127,9 +127,9 @@ def addScanParameter(self, name, start, end, points, log=False, slave=False):
         - float(end) = upper bound of scan
         - int(points) = number of points in scan range
         - bool(log) = Use a logarithmic (base10) range
-        - bool(slave) = Scan parameters can be masters i.e. an independent axis or a "slave" which moves synchronously with the previously defined parameter range.
+        - bool(follower) = Scan parameters can be leaders i.e. an independent axis or a "follower" which moves synchronously with the previously defined parameter range.
 
-        The first ScanParameter cannot be a slave.
+        The first ScanParameter cannot be a follower.
         """
         offset = 1
         assert self.testInputParameter(name), (
@@ -140,22 +140,24 @@ def addScanParameter(self, name, start, end, points, log=False, slave=False):
         ), '\nSCANNER: This operation is currently not allowed\n'
         if not len(self.GenOrder) == 0:
             for el in self.GenOrder:
-                if self.GenDict[el][4] == False:  # test if not slave
+                if self.GenDict[el][4] == False:  # test if not follower
                     offset = offset * self.GenDict[el][2]  # increment offset
-            if slave == True:
-                prevpar = self.GenOrder[-1]  # previous parameter, i.e. master
-                offset = self.GenDict[prevpar][5]  # don't increment for slave
+            if follower == True:
+                prevpar = self.GenOrder[-1]  # previous parameter, i.e. leader
+                offset = self.GenDict[prevpar][5]  # don't increment for follower
                 if points != self.GenDict[prevpar][2]:
                     print(
-                        'SCANNER: Slave parameter needs to iterate over same number of\npoints as master...resetting points.'
+                        'SCANNER: Follower parameter needs to iterate over same number of\npoints as leader...resetting points.'
                     )
                     points = self.GenDict[prevpar][2]
         else:
-            if slave == True:
-                slave = False
-                print('SCANNER: Inner range cannot be a slave ... resetting to master')
+            if follower == True:
+                follower = False
+                print(
+                    'SCANNER: Inner range cannot be a follower ... resetting to leader'
+                )
         self.GenDict.setdefault(
-            name, (start, end, points, log, slave, offset, getattr(self.mod, name))
+            name, (start, end, points, log, follower, offset, getattr(self.mod, name))
         )
         setattr(self, name + '_test', self.stepGen(offset))
         setattr(self, name, self.rangeGen(name, start, end, points, log))
@@ -269,7 +271,7 @@ def Run(self, ReRun=False):
             # self.mod.mode_state_nan_on_fail = True
         Tsteps = 1
         for gen in self.GenOrder:
-            if self.GenDict[gen][4] == False:  # don't increase Tsteps for slaves
+            if self.GenDict[gen][4] == False:  # don't increase Tsteps for follower
                 Tsteps *= self.GenDict[gen][2]
         print(next(self.scanT.RUN))
         analysis_counter = 0

diff --git a/pysces/examples/testRunScatter.py b/pysces/examples/testRunScatter.py
@@ -2,29 +2,30 @@
 # Testing the new parallel scanner class
 
 import os
+
 backupdir = os.getcwd()
 
 import numpy as np
 import pysces
 
-tbox=pysces.PyscesUtils.TimerBox()
+tbox = pysces.PyscesUtils.TimerBox()
 import time
 
-m=pysces.model('isola2a')
+m = pysces.model('isola2a')
 
 print("\n\nParallel execution...using RunScatter")
 par2 = pysces.ParScanner(m)
-t5=time.time()
-par2.addScanParameter('V4',60,100,11)
-par2.addScanParameter('V1',100,130,16)
-par2.addScanParameter('V2',100,130,16,slave=True)
-par2.addScanParameter('V3',80,90,6)
+t5 = time.time()
+par2.addScanParameter('V4', 60, 100, 11)
+par2.addScanParameter('V1', 100, 130, 16)
+par2.addScanParameter('V2', 100, 130, 16, follower=True)
+par2.addScanParameter('V3', 80, 90, 6)
 par2.addUserOutput('J_R1', 'A', 'ecR4_X', 'ccJR1_R1')
-#par2.addUserOutput('J_R1', 'A')
+# par2.addUserOutput('J_R1', 'A')
 par2.RunScatter()
-t6=time.time()
-print("Duration: %.2f seconds" % (t6-t5))
-par2.statespersecond = par2.Tsteps/(t6-t5)
+t6 = time.time()
+print("Duration: %.2f seconds" % (t6 - t5))
+par2.statespersecond = par2.Tsteps / (t6 - t5)
 print("States per second: %.1f" % par2.statespersecond)
 
-os.chdir(backupdir)
+os.chdir(backupdir)
diff --git a/pysces/examples/testparscanner.py b/pysces/examples/testparscanner.py
@@ -2,76 +2,80 @@
 # Testing the new parallel scanner class
 
 import os
+
 backupdir = os.getcwd()
 
 import numpy as np
 import pysces
 
-tbox=pysces.PyscesUtils.TimerBox()
+tbox = pysces.PyscesUtils.TimerBox()
 import time
 
-m=pysces.model('isola2a')
+m = pysces.model('isola2a')
 
 ser = pysces.Scanner(m)
 
 print("Serial execution...")
 print("Start: ", tbox.normal_timer('SER'))
 print(next(tbox.SER))
-t1=time.time()
+t1 = time.time()
 ser.quietRun = True
-ser.addScanParameter('V4',60,100,11)
-ser.addScanParameter('V1',100,160,16)
-ser.addScanParameter('V2',100,130,16,slave=True)
-ser.addScanParameter('V3',80,90,6)
-ser.addUserOutput('J_R1', 'A', 'ecR4_X','ccJR1_R1')
-#ser.addUserOutput('J_R1', 'A')
+ser.addScanParameter('V4', 60, 100, 11)
+ser.addScanParameter('V1', 100, 160, 16)
+ser.addScanParameter('V2', 100, 130, 16, follower=True)
+ser.addScanParameter('V3', 80, 90, 6)
+ser.addUserOutput('J_R1', 'A', 'ecR4_X', 'ccJR1_R1')
+# ser.addUserOutput('J_R1', 'A')
 ser.Run()
 print("Done: ", next(tbox.SER))
-t2=time.time()
-print("Duration: %.2f seconds" % (t2-t1))
-ser.statespersecond = len(ser.ScanSpace)/(t2-t1)
+t2 = time.time()
+print("Duration: %.2f seconds" % (t2 - t1))
+ser.statespersecond = len(ser.ScanSpace) / (t2 - t1)
 print("States per second: %.1f" % ser.statespersecond)
 
 print("\n\nParallel execution...scans per run =", 100)
 par = pysces.ParScanner(m)
 par.scans_per_run = 100
-t3=time.time()
-par.addScanParameter('V4',60,100,11)
-par.addScanParameter('V1',100,160,16)
-par.addScanParameter('V2',100,130,16,slave=True)
-par.addScanParameter('V3',80,90,6)
+t3 = time.time()
+par.addScanParameter('V4', 60, 100, 11)
+par.addScanParameter('V1', 100, 160, 16)
+par.addScanParameter('V2', 100, 130, 16, follower=True)
+par.addScanParameter('V3', 80, 90, 6)
 par.addUserOutput('J_R1', 'A', 'ecR4_X', 'ccJR1_R1')
-#par.addUserOutput('J_R1', 'A')
+# par.addUserOutput('J_R1', 'A')
 par.Run()
-t4=time.time()
-print("Duration: %.2f seconds" % (t4-t3))
-par.statespersecond = par.Tsteps/(t4-t3)
+t4 = time.time()
+print("Duration: %.2f seconds" % (t4 - t3))
+par.statespersecond = par.Tsteps / (t4 - t3)
 print("States per second: %.1f" % par.statespersecond)
 
-print("\n Speedup with load balanced TaskClient: %.2f" % (par.statespersecond/ser.statespersecond))
+print(
+    "\n Speedup with load balanced TaskClient: %.2f"
+    % (par.statespersecond / ser.statespersecond)
+)
 
 print("\n\nParallel execution...using RunScatter")
 par2 = pysces.ParScanner(m)
-t5=time.time()
-par2.addScanParameter('V4',60,100,11)
-par2.addScanParameter('V1',100,160,16)
-par2.addScanParameter('V2',100,130,16,slave=True)
-par2.addScanParameter('V3',80,90,6)
+t5 = time.time()
+par2.addScanParameter('V4', 60, 100, 11)
+par2.addScanParameter('V1', 100, 160, 16)
+par2.addScanParameter('V2', 100, 130, 16, follower=True)
+par2.addScanParameter('V3', 80, 90, 6)
 par2.addUserOutput('J_R1', 'A', 'ecR4_X', 'ccJR1_R1')
-#par2.addUserOutput('J_R1', 'A')
+# par2.addUserOutput('J_R1', 'A')
 par2.RunScatter()
-t6=time.time()
-print("Duration: %.2f seconds" % (t6-t5))
-par2.statespersecond = par2.Tsteps/(t6-t5)
+t6 = time.time()
+print("Duration: %.2f seconds" % (t6 - t5))
+par2.statespersecond = par2.Tsteps / (t6 - t5)
 print("States per second: %.1f" % par2.statespersecond)
 
-print("\n Speedup with RunScatter: %.2f" % (par2.statespersecond/ser.statespersecond))
+print("\n Speedup with RunScatter: %.2f" % (par2.statespersecond / ser.statespersecond))
 
 print("\n===========\nComparing results...")
-#comp = np.equal(ser.SteadyStateResults, par.SteadyStateResults[::5])
-#print np.alltrue(comp)
-#comp2 = np.equal(ser.UserOutputResults, par.UserOutputResults[::5])
-#print np.alltrue(comp)
+# comp = np.equal(ser.SteadyStateResults, par.SteadyStateResults[::5])
+# print np.alltrue(comp)
+# comp2 = np.equal(ser.UserOutputResults, par.UserOutputResults[::5])
+# print np.alltrue(comp)
 
 sss = ser.SteadyStateResults
 pss = par.SteadyStateResults
@@ -80,10 +84,10 @@
 p2ss = par2.SteadyStateResults
 p2uo = par2.UserOutputResults
 
-print("serial vs. parallel s/s results     : ", np.alltrue(np.equal(sss,pss)))
-print("serial vs. parallel user output     : ", np.alltrue(np.equal(suo,puo)))
-print("TaskClient vs RunScatter s/s results: ", np.alltrue(np.equal(pss,p2ss)))
-print("TaskClient vs RunScatter user output: ", np.alltrue(np.equal(puo,p2uo)))
+print("serial vs. parallel s/s results     : ", np.alltrue(np.equal(sss, pss)))
+print("serial vs. parallel user output     : ", np.alltrue(np.equal(suo, puo)))
+print("TaskClient vs RunScatter s/s results: ", np.alltrue(np.equal(pss, p2ss)))
+print("TaskClient vs RunScatter user output: ", np.alltrue(np.equal(puo, p2uo)))
 
 
-os.chdir(backupdir)
+os.chdir(backupdir)