Resuming a calculation with hot chains (-nc)

PTMCMCSampler/PTMCMCSampler.py

@@ -1,6 +1,7 @@
 import os
 import sys
 import time
+import warnings
 
 import numpy as np
 
@@ -69,6 +70,8 @@ class PTSampler(object):
     @param outDir: Full path to output directory for chain files (default = ./chains)
     @param verbose: Update current run-status to the screen (default=True)
     @param resume: Resume from a previous chain (still in testing so beware) (default=False)
+    @param ihcwr: Ignore hot chains when resuming. Note, hot chains will enter a burn-in 
+    phase when resuming (default=False)
 
     """
 
@@ -89,6 +92,7 @@ def __init__(
         outDir="./chains",
         verbose=True,
         resume=False,
+        ihcwr=False,
         seed=None,
     ):
         # MPI initialization
@@ -117,6 +121,7 @@ def __init__(
         self.outDir = outDir
         self.verbose = verbose
         self.resume = resume
+        self.ignoreHotChainsWhenResuming = ihcwr
 
         # setup output file
         if not os.path.exists(self.outDir):
@@ -297,16 +302,23 @@ def initialize(
             except ValueError as error:
                 print("Reading old chain files failed with error", error)
                 raise Exception("Couldn't read old chain to resume")
-            self._chainfile = open(self.fname, "a")
+                
             if (
                 self.isave != self.thin
                 and self.resumeLength % (self.isave / self.thin) != 1  # This special case is always OK
             ):  # Initial sample plus blocks of isave/thin
-                raise Exception(
-                    (
-                        "Old chain has {0} rows, which is not the initial sample plus a multiple of isave/thin = {1}"
-                    ).format(self.resumeLength, self.isave // self.thin)
-                )
+                if self.MPIrank != 0 and self.writeHotChains is False and self.ignoreHotChainsWhenResuming:
+                    warnings.warn("Neglecting hot chains from the previous run. It is recommended to set writeHotChains=True when resuming a run with multiple temperatures.")
+                    self._chainfile = open(self.fname, "w")
+                else:
+                    raise Exception(
+                        (
+                            "Old chain has {0} rows, which is not the initial sample plus a multiple of isave/thin = {1}"
+                        ).format(self.resumeLength, self.isave // self.thin)
+                    )
+            else:
+                self._chainfile = open(self.fname, "a")
+
             print(
                 "Resuming with",
                 self.resumeLength,