Merge branch 'master' of github.com:esemble/simpy

lib/e_2_pdb.py

@@ -5,7 +5,7 @@
 import argparse
 from mytype import System, Molecule, Atom
 from pdb import Pdb
-from output_conf import toReaxLammps, toGeo, toPdb, toMsd, toXyz, toMusic, toPoscar, toJdft, toCfg
+from output_conf import toReaxLammps, toGeo, toPdb, toMsd, toXyz, toMusic, toPoscar, toJdft, toCfg, toTowheecoords
 
 def usage():
     print """python e_2_pdb [pbc|nopbc]
@@ -58,6 +58,7 @@ def withPbc(testfile="supper.pdb", args=''):
     toPoscar(b,)
     toCfg(b,)
     toJdft(b,)
+    toTowheecoords(b)
     if args:
         if args.element:
             toPdb(b, "out.pdb", 1)

lib/output_conf.py

@@ -646,3 +646,20 @@ def toCfg(system, outfile="out.cfg"):
             o.write("%20.15f%20.15f%20.15f\n"%(xf, yf, zf))
     o.close()
 
+def toTowheecoords(system, outfile="towhee_coords"):
+    """ output to towhee_coords file format
+    """
+    o = open(outfile, 'w')
+    for i in system.atoms:
+        line = ''
+        line += "%25.15f"%i.x[0]
+        line += "%25.15f"%i.x[1]
+        line += "%25.15f"%i.x[2]
+        if len(i.element) > 0:
+            line += "%10s"%i.element
+        else:
+            line += "%10s"%i.name
+        line += "\n"
+        o.write(line)
+    o.close()
+

tools/linux/cmdall

@@ -32,7 +32,10 @@ def exec_folders(dlist, cmd, args):
                 print "cmd processing in %s"%os.getcwd()
             if args.arg:
                 folder = os.path.basename(os.getcwd())
-                run += " %s"%folder
+                print folder
+                run = run.replace("xx", folder)
+            if args.v:
+                print "cmd is %s"%run
             os.system(run)
             os.chdir("..")
 

tools/stampede2/job.py

@@ -4,29 +4,47 @@
 
 run_jobs = []
 wait_jobs = []
+complete_or_err_jobs = []
+block_jobs = []
 total_jobs = ""
 
+end_flag = 0
 f = os.popen("showq -u")
 for i in f:
     if i.strip().startswith("ACTIVE JOBS"):
         break
 for i in f:
     if i.strip().startswith("WAITING JOBS"):
         break
-    if i.strip().startswith("Total Jobs"):
-	totoal_jobs = i
-        break
     run_jobs.append(i)
+
 for i in f:
-    if i.strip().startswith("COMPLETING/ERRORED JOBS"):
+    if i.strip().startswith("COMPLETING"):
+        break
+    if i.strip().startswith("BLOCKED JOBS"):
         break
     if i.strip().startswith("Total Jobs"):
-	totoal_jobs = i
+        end_flag = 1
+        total_jobs = i
         break
     wait_jobs.append(i)
 
-#print run_jobs
-#print wait_jobs
+for i in f:
+    if i.strip().startswith("BLOCKED JOBS"):
+        break
+    if i.strip().startswith("Total Jobs"):
+        end_flag = 1
+        total_jobs = i
+        break
+    complete_or_err_jobs.append(i)
+
+if not end_flag:
+    for i in f:
+        if i.strip().startswith("Total Jobs"):
+	    total_jobs = i
+            break
+        block_jobs.append(i)
+
 f.close()
 
 if len(run_jobs) > 3:
@@ -47,8 +65,8 @@
         for j in f:
             if j.strip().startswith("WorkDir"):
                 tokens = j.strip().split()
-                workfolder = tokens[0].split("=")[1][21:]
-                workfolder = "~" + workfolder
+                workfolder = tokens[0].split("=")[1]
+                #workfolder = "~" + workfolder
                 break
         print workfolder
         f.close()
@@ -71,6 +89,24 @@
         print workfolder
         f.close()
 
+if len(block_jobs) > 3:
+    print "-"*20,
+    print "Jobs blocking",
+    print "-"*20
+    for i in block_jobs[2:-1]:
+        tokens = i.strip().split()
+        jobid = tokens[0]
+        print jobid, 
+        f = os.popen("scontrol show job %s"%jobid)
+        for j in f:
+            if j.strip().startswith("WorkDir"):
+                tokens = j.strip().split()
+                workfolder = tokens[0].split("=")[1][21:]
+                workfolder = "~" + workfolder
+                break
+        print workfolder
+        f.close()
+
 print "-"*20,
 print "Jobs summary",
 print "-"*20

tools/stampede2/tocheng-ion.py

@@ -0,0 +1,23 @@
+#!/usr/bin/env python
+
+import os
+import sys
+import argparse
+
+def main():
+    parser = argparse.ArgumentParser()
+    parser.add_argument("fname", nargs="+", help="geo file name")
+    parser.add_argument("-o", default="/net/hulk/PMD/tcheng/download", help="convert the file to other formats (geo, xyz, gjf, lammps)")
+    args = parser.parse_args()
+    files = args.fname
+    folder = args.o
+    ip = "ion.wag.caltech.edu"
+    usr = "chengtao"
+    cmd = "scp -r "
+    cmd += " ".join(files)
+    cmd += " "+usr+"@"+ip+":"+folder
+    os.system(cmd)
+
+if __name__ == "__main__":
+    main()
+