[cig-commits] [commit] master: Add ability to combine "heating" output (7ca37a6)

[cig_noreply at geodynamics.org]

Repository : ssh://geoshell/citcoms

On branch  : master
Link       : https://github.com/geodynamics/citcoms/compare/c770f8e2897398470734bc655d8a155819f81c57...fb1839e7e93bc56eb542afd64b3db70f2df6a5d8

>---------------------------------------------------------------

commit 7ca37a6c25611762a837e3dc34223e283d66aaac
Author: karredondo <karredondo at ucdavis.edu>
Date:   Fri Feb 14 14:30:31 2014 -0800

    Add ability to combine "heating" output
    
    Katrina Arredondo
    
    Heating output is in terms of elements instead of nodes. The data is
    placed in a third combine file "ele" aside from "cap" and "opt."


>---------------------------------------------------------------

7ca37a6c25611762a837e3dc34223e283d66aaac
 visual/autocombine.py  | 27 ++++++++++++++++++++++++++-
 visual/batchcombine.py |  2 +-
 visual/combine.py      | 46 +++++++++++++++++++++++++++++++++++++++++++++-
 3 files changed, 72 insertions(+), 3 deletions(-)

diff --git a/visual/autocombine.py b/visual/autocombine.py
old mode 100755
new mode 100644
index 9f3ad20..604e544
--- a/visual/autocombine.py
+++ b/visual/autocombine.py
@@ -34,6 +34,7 @@ usage: autocombine.py machinefile inputfile step1 [step2 [...] ]
 # default values for CitcomS input
 defaults = {'output_format': 'ascii',
             'output_optional': 'surf,botm',
+	    'output_optional_EL': 'heating',
             'buoy_type': 1,
             'tracer_flavors': 2,
             'nprocx': 1,
@@ -53,12 +54,26 @@ def normalize_optional(output_optional):
         opt = opt.strip()
 
         ## retain fields that are node-based
-        if opt in ('pressure', 'stress', 'comp_nd'):
+        if opt in ('pressure', 'stress', 'comp_nd','phase'):
             fields.append(opt)
 
 
     return ','.join(fields)
 	
+def normalize_optional_EL(output_optional_EL):
+    fields = []
+
+    for opt_EL in output_optional_EL.split(','):
+        ## remove the leading/trailing whitespaces
+        opt_EL = opt_EL.strip()
+
+        ## retain fields that are node-based
+        if opt_EL in ('heating'):
+            fields.append(opt_EL)
+
+
+    return ','.join(fields)
+
 
 
 if __name__ == '__main__':
@@ -91,6 +106,9 @@ if __name__ == '__main__':
     output_optional = parser.getstr('output_optional')
     optional_fields = normalize_optional(output_optional)
 	
+    output_optional_EL = parser.getstr('output_optional_EL')
+    optional_fields_EL = normalize_optional_EL(output_optional_EL)
+
     buoy_type = parser.getint('buoy_type')
     nflavors = parser.getint('tracer_flavors')
     if buoy_type == 0:
@@ -129,6 +147,13 @@ if __name__ == '__main__':
                             ncap, nprocx, nprocy, nprocz,
                             optional_fields, ncompositions)
 							
+		# combining optional fields (based on element number), if necessary
+        if optional_fields_EL:
+            bc.batchcombine(nodelist, datadir, datafile, timestep,
+                            (nodex - 1), (nodey-1), (nodez-1),
+                            ncap, (nprocx - 0), (nprocy-0), (nprocz - 0),
+                            optional_fields_EL, ncompositions)
+
 
 
 # version
diff --git a/visual/batchcombine.py b/visual/batchcombine.py
old mode 100755
new mode 100644
index 280488f..9bfb847
--- a/visual/batchcombine.py
+++ b/visual/batchcombine.py
@@ -81,7 +81,7 @@ def batchpaste(datadir, datafile, fields, timestep, nodes):
     cwd = os.getcwd()
 
     for rank, node in enumerate(nodes):
-        if node == 'localhost' or node == '-' or node == hostname:
+        if node == 'localhost' or node == hostname:
             # local paste
             import pasteCitcomData
             pasteCitcomData.run(datadir, datafile, fields, rank, timestep, cwd)
diff --git a/visual/combine.py b/visual/combine.py
index 232a3fe..a159856 100755
--- a/visual/combine.py
+++ b/visual/combine.py
@@ -101,6 +101,45 @@ class Combine(object):
 
 
 
+    def join_EL(self, data, me):
+        # processor geometry
+        nprocx = self.nprocx
+        nprocy = self.nprocy
+        nprocz = self.nprocz
+
+        mylocz = me % nprocz
+        mylocx = ((me - mylocz) / nprocz) % nprocx
+        mylocy = (((me - mylocz) / nprocz - mylocx) / nprocx) % nprocy
+
+        # mesh geometry
+        nodex = self.nodex
+        nodey = self.nodey
+        nodez = self.nodez
+
+        mynodex = 1 + (nodex-nprocx)/nprocx
+        mynodey = 1 + (nodey-nprocy)/nprocy
+        mynodez = 1 + (nodez-nprocz)/nprocz
+
+        if not len(data) == mynodex * mynodey * mynodez:
+            raise ValueError, "incorrect data size"
+
+
+        mynxs = (mynodex - 0) * mylocx
+        mynys = (mynodey - 0) * mylocy
+        mynzs = (mynodez - 0) * mylocz
+
+        n = 0
+        for i in range(mynys, mynys+mynodey):
+            for j in range(mynxs, mynxs + mynodex):
+                for k in range(mynzs, mynzs + mynodez):
+                    m = k + j * nodez + i * nodex * nodez
+                    self.saved[m] = data[n]
+                    n += 1
+
+        return
+
+
+
     def write(self, filename):
         fp = file(filename, 'w')
         header = '%d x %d x %d\n' % (self.nodex, self.nodey, self.nodez)
@@ -124,10 +163,15 @@ def combine(prefix, opts, step, nodex, nodey, nodez,
             filename = '%s.%s.%d.%d.pasted' % (prefix, opts, n, step)
             print 'reading', filename
             data = cb.readData(filename, 0)
-            cb.join(data, n)
+	    if opts == 'heating':
+		cb.join_EL(data, n)
+	    else:
+            	cb.join(data, n)
 
         if opts == 'coord,velo,visc':
             filename = '%s.cap%02d.%d' % (prefix, i, step)
+	elif opts == 'heating':
+	    filename = '%s.ele%02d.%d' % (prefix, i, step)
         else:
             filename = '%s.opt%02d.%d' % (prefix, i, step)