moved __seed to system class, handling tcl arrays in h5md write

espressomd · May 25, 2016 · 2ad7c1f · 2ad7c1f
1 parent 8e8d1d0
commit 2ad7c1f
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Showing 4 changed files with 24 additions and 10 deletions.
diff --git a/scripts/h5md.tcl b/scripts/h5md.tcl
@@ -470,8 +470,12 @@ proc dump_script_to_h5md {} {
         h5mdfile H5Dcreate2 "parameters/files/tclvariables"
         h5mdfile H5Dopen2 "parameters/files/tclvariables"
         for { set i 0 } { $i < [llength $which] } { incr i } {
-            h5mdfile H5_write_value value [lindex $which $i] index $i 0 
-            h5mdfile H5_write_value value [set ::[lindex $which $i]] index $i 1
+            if {[array exists ::[lindex $which $i] ]==0 } {
+                    h5mdfile H5_write_value value [lindex $which $i] index $i 0 
+                    h5mdfile H5_write_value value [set ::[lindex $which $i]] index $i 1
+            } else {
+                puts "Did not write tcl array variable [lindex $which $i] to h5md dataset"    
+            }
         }
         h5mdfile H5Dwrite
     }

diff --git a/src/python/espressomd/_system.pyx b/src/python/espressomd/_system.pyx
@@ -33,7 +33,6 @@ from cellsystem import CellSystem
 
 import sys
 
-__seed=-10
 setable_properties = ["box_l", "max_num_cells", "min_num_cells",
                       "node_grid", "npt_piston", "npt_p_diff",
                       "periodicity", "skin", "time",
@@ -373,12 +372,11 @@ cdef class System:
         def __get__(self):
             return max_cut_bonded
 
+    __seed=None
     property seed:
         def __set__(self, _seed):
-            print(_seed)
             cdef vector[int] seed_array
-            global __seed
-            __seed = _seed
+            self.__seed = _seed
             if(isinstance(_seed, int) and self.n_nodes == 1):
                 seed_array.resize(1)
                 seed_array[0] = int(_seed)
@@ -397,7 +395,7 @@ cdef class System:
                     "The seed has to be an integer or a list of integers with one integer per node")
 
         def __get__(self):
-            return __seed
+            return self.__seed
 
     def change_volume_and_rescale_particles(d_new, dir="xyz"):
         """Change box size and rescale particle coordinates

diff --git a/src/python/espressomd/diamond.pyx b/src/python/espressomd/diamond.pyx
@@ -55,8 +55,6 @@ cdef class Diamond:
                 "Please define a bonded interaction [0] before setting up polymers!")
 
     def __set_params_in_es_core(self):
-        print(self._params["a"], self._params["bond_length"], self._params["MPC"], self._params["N_CI"], self._params[
-              "val_nodes"], self._params["val_cM"], self._params["val_CI"], self._params["cM_dist"], self._params["nonet"])
         return diamondC(self._params["a"], self._params["bond_length"], self._params["MPC"], self._params["N_CI"], self._params["val_nodes"], self._params["val_cM"], self._params["val_CI"], self._params["cM_dist"], self._params["nonet"])
 
     def _set_params_in_es_core(self):

diff --git a/testsuite/tcl/nsquare.tcl b/testsuite/tcl/nsquare.tcl
@@ -57,6 +57,19 @@ proc write_data {file} {
     blockfile $f write bonds
     close $f
 }
+proc write_data_h5_old_data {path} {
+	h5md_init $path
+	h5md_write_positions;# write OLD positions by hand as we need the OLD positions
+}
+
+proc write_data_h5_new_data {path} {
+	energy [analyze energy total]
+	pressure [analyze pressure total]
+	verlet_reuse [setmd verlet_reuse]
+	h5md_write_forces
+}
+
+
 
 if { [catch {
     ############## integ-specific part
@@ -68,6 +81,7 @@ if { [catch {
     inter 0 fene $fene_k $fene_r
 
     read_data "intpbc_system.data.gz"
+    write_data_h5_old_data "../test_data/nsquare_test_data.h5"
 
     for { set i 0 } { $i <= [setmd max_part] } { incr i } {
 	set F($i) [part $i pr f]
@@ -82,7 +96,7 @@ if { [catch {
 
     # here you can create the necessary snapshot
     # write_data "intpbc_system.data.gz"
-
+    write_data_h5_old_data "../test_data/"
     ############## end
 
     set toteng [analyze energy total]