diff --git a/tools/modify_fates_paramfile.py b/tools/modify_fates_paramfile.py
index 92ab14dab1..53bd82decc 100755
--- a/tools/modify_fates_paramfile.py
+++ b/tools/modify_fates_paramfile.py
@@ -19,6 +19,8 @@
 from scipy.io import netcdf as nc
 import argparse
 import shutil
+import tempfile
+
 
 # ========================================================================================
 # ========================================================================================
@@ -38,60 +40,74 @@ def main():
     parser.add_argument('--silent', '--s', dest='silent', help="prevent writing of output.", action="store_true")
     #
     args = parser.parse_args()
-    # print(args.varname, args.pftnum, args.inputfname, args.outputfname, args.val, args.overwrite)
-    #
-    # check to see if output file exists
-    if os.path.isfile(args.outputfname):
-        if args.overwrite:
-            if not args.silent:
-                print('replacing file: '+args.outputfname)
-            os.remove(args.outputfname)
-        else:
-            raise ValueError('Output file already exists and overwrite flag not specified for filename: '+args.outputfname)
-    #
-    shutil.copyfile(args.inputfname, args.outputfname)
-    #
-    ncfile = nc.netcdf_file(args.outputfname, 'a')
     #
-    var = ncfile.variables[args.varname]
+    # work with the file in some random temprary place so that if something goes wrong nothing happens to original file and it doesn't make an output file
+    tempdir = tempfile.mkdtemp()
+    tempfilename = os.path.join(tempdir, 'temp_fates_param_file.nc')
     #
-    ### check to make sure that, if a PFT is specified, the variable has a PFT dimension, and if not, then it doesn't. and also that shape is reasonable.
-    ndim_file = len(var.dimensions)
-    ispftvar = False
-    for i in range(ndim_file):
-        if var.dimensions[i] == 'fates_pft':
-            ispftvar = True
-            npft_file = var.shape[i]
-            pftdim = 0
-        else:
-            npft_file = None
-            pftdim = None
-    if args.pftnum == None and ispftvar:
-        raise ValueError('pft value is missing but variable has pft dimension.')
-    if args.pftnum != None and not ispftvar:
-        raise ValueError('pft value is present but variable does not have pft dimension.')
-    if ndim_file > 1:
-        raise ValueError('variable dimensionality is too high for this script')
-    if ndim_file == 1 and not ispftvar:
-        raise ValueError('variable dimensionality is too high for this script')
-    if args.pftnum != None and ispftvar:
-        if args.pftnum > npft_file:
-            raise ValueError('PFT specified ('+str(args.pftnum)+') is larger than the number of PFTs in the file ('+str(npft_file)+').')
-        if pftdim == 0:
+    try:
+        shutil.copyfile(args.inputfname, tempfilename)
+        #
+        ncfile = nc.netcdf_file(tempfilename, 'a')
+        #
+        var = ncfile.variables[args.varname]
+        #
+        ### check to make sure that, if a PFT is specified, the variable has a PFT dimension, and if not, then it doesn't. and also that shape is reasonable.
+        ndim_file = len(var.dimensions)
+        ispftvar = False
+        # for purposes of current stat eof this script, assume 1D 
+        if ndim_file > 1:
+            raise ValueError('variable dimensionality is too high for this script')
+        if ndim_file < 1:
+            raise ValueError('variable dimensionality is too low for this script. FATES assumes even scalars have a 1-length dimension')
+        for i in range(ndim_file):
+            if var.dimensions[i] == 'fates_pft':
+                ispftvar = True
+                npft_file = var.shape[i]
+                pftdim = 0
+            elif var.dimensions[i] == 'fates_scalar':
+                npft_file = None
+                pftdim = None
+            else:
+                raise ValueError('variable is not on either the PFT or scalar dimension')
+        if args.pftnum == None and ispftvar:
+            raise ValueError('pft value is missing but variable has pft dimension.')
+        if args.pftnum != None and not ispftvar:
+            raise ValueError('pft value is present but variable does not have pft dimension.')
+        if args.pftnum != None and ispftvar:
+            if args.pftnum > npft_file:
+                raise ValueError('PFT specified ('+str(args.pftnum)+') is larger than the number of PFTs in the file ('+str(npft_file)+').')
+            if pftdim == 0:
+                if not args.silent:
+                    print('replacing prior value of variable '+args.varname+', for PFT '+str(args.pftnum)+', which was '+str(var[args.pftnum-1])+', with new value of '+str(args.val))
+                var[args.pftnum-1] = args.val
+        elif args.pftnum == None and not ispftvar:
             if not args.silent:
-                print('replacing prior value of variable '+args.varname+', for PFT '+str(args.pftnum)+', which was '+str(var[args.pftnum-1])+', with new value of '+str(args.val))
-            var[args.pftnum-1] = args.val
-    elif args.pftnum == None and not ispftvar:
-        if not args.silent:
-            print('replacing prior value of variable '+args.varname+', which was '+str(var[:])+', with new value of '+str(args.val))
-        var[:] = args.val
-    else:
-        raise ValueError('Nothing happened somehow.')
-    #
-    #
-    ncfile.close()
-
-
+                print('replacing prior value of variable '+args.varname+', which was '+str(var[:])+', with new value of '+str(args.val))
+            var[:] = args.val
+        else:
+            raise ValueError('Nothing happened somehow.')
+        #
+        #
+        ncfile.close()
+        #
+        #
+        # now move file from temprary location to final location
+        #
+        # check to see if output file exists
+        if os.path.isfile(args.outputfname):
+            if args.overwrite:
+                if not args.silent:
+                    print('replacing file: '+args.outputfname)
+                os.remove(args.outputfname)
+            else:
+                raise ValueError('Output file already exists and overwrite flag not specified for filename: '+args.outputfname)
+        #
+        shutil.move(tempfilename, args.outputfname)
+        shutil.rmtree(tempdir, ignore_errors=True)
+    except:
+        shutil.rmtree(tempdir, ignore_errors=True)
+        raise
 
 
 # =======================================================================================