Merge pull request #27 from ICAMS/update/ts

enable separate switching times for fe and ts modes

calphy/input.py

@@ -121,6 +121,8 @@ def read_yamlfile(file):
         #eqbr and switching time
         "te": 25000,
         "ts": 50000,
+        #enable separate switching time for rs
+        "ts_rs": 50000,
         "tguess": None,
         "dtemp": 200,
         "maxattempts": 5,
@@ -171,6 +173,15 @@ def read_yamlfile(file):
     options["md"]["pair_style"] = check_and_convert_to_list(indata["md"]["pair_style"])
     options["md"]["pair_coeff"] = fix_paths(check_and_convert_to_list(indata["md"]["pair_coeff"]))
 
+    #now modify ts;
+    if isinstance(options["md"]["ts"], list):
+        ts1 = options["md"]["ts"][0]
+        ts2 = options["md"]["ts"][1]
+        options["md"]["ts"] = ts1
+        options["md"]["ts_rs"] = ts2
+    else:
+        options["md"]["ts_rs"] = options["md"]["ts"]
+
     if not len(options["element"]) == len(options["mass"]):
         raise ValueError("length of elements and mass should be same!")
     options["nelements"] = len(options["element"])

calphy/phase.py

@@ -344,7 +344,7 @@ def reversible_scaling(self, iteration=1):
             lmp.command("dump              d1 all custom %d traj.forward_%d.dat id type mass x y z vx vy vz"%(self.options["md"]["traj_interval"],
                 iteration))
 
-        lmp.command("run               %d"%self.options["md"]["ts"])
+        lmp.command("run               %d"%self.options["md"]["ts_rs"])
 
         #unfix
         lmp.command("unfix             f3")
@@ -401,7 +401,7 @@ def reversible_scaling(self, iteration=1):
             lmp.command("dump              d1 all custom %d traj.backward_%d.dat id type mass x y z vx vy vz"%(self.options["md"]["traj_interval"],
                 iteration))
 
-        lmp.command("run               %d"%self.options["md"]["ts"])
+        lmp.command("run               %d"%self.options["md"]["ts_rs"])
 
         lmp.command("unfix             f3")
         lmp.command("unfix             f1")