changes to python-pyrex simulator interface

author: Eric Messick <ericm@nanorex.com> 2008-01-24 05:59:06 +0000
committer: Eric Messick <ericm@nanorex.com> 2008-01-24 05:59:06 +0000
commit: 4e0cd140c2144dda21cff23d81afc450c8c5d2b3 (patch)
tree: 6a5ed69f98664ff8b72dbe25bb621f35c4ed37b7 /sim
parent: 93027d05c213b3092c624b6ee45543c2b9e1cf89 (diff)
download: nanoengineer-4e0cd140c2144dda21cff23d81afc450c8c5d2b3.tar.gz
nanoengineer-4e0cd140c2144dda21cff23d81afc450c8c5d2b3.zip
10 files changed, 252 insertions, 726 deletions
diff --git a/sim/src/globals.c b/sim/src/globals.c
index 66472bfb6..cacf3f77e 100755
--- a/sim/src/globals.c
+++ b/sim/src/globals.c
@@ -59,7 +59,8 @@ double ThermostatGamma;
 double ThermostatG1;
 
 // absolute distance in nm beyond which gromacs will consider vdW
-// forces to be exactly zero.
+// forces to be exactly zero.  If less than zero, user defined tables
+// will not be used, and a default value of 1.0 nm will be used.
 double VanDerWaalsCutoffRadius;
 
 // multiple of rvdW where interpolation table ends, and van der Waals
@@ -130,7 +131,7 @@ reinit_globals(void)
     NumFrames = 100;
     DumpAsText = 0;
     DumpIntermediateText = 0;
-    PrintFrameNums = 1;
+    PrintFrameNums = 0;
     OutputFormat = 1;
     KeyRecordInterval = 32;
     DirectEvaluate = 0;
@@ -155,7 +156,7 @@ reinit_globals(void)
     MinimizeThresholdEndRMS = 1.0;
     MinimizeThresholdEndMax = 0.0; // set by constrainGlobals, below
 
-    VanDerWaalsCutoffRadius = 1.0; // (nm) default for atomic minimization
+    VanDerWaalsCutoffRadius = -1.0; // use gromacs built in functions
     VanDerWaalsCutoffFactor = 1.7;
 
     EnableElectrostatic = 1;
@@ -223,9 +224,16 @@ printGlobals()
         write_traceline("# MinimizeThresholdEndRMS: %f\n", MinimizeThresholdEndRMS);
         write_traceline("# MinimizeThresholdEndMax: %f\n", MinimizeThresholdEndMax);
     }
+    write_traceline("# VanDerWaalsCutoffRadius: %f\n", VanDerWaalsCutoffRadius);
     write_traceline("# VanDerWaalsCutoffFactor: %f\n", VanDerWaalsCutoffFactor);
     write_traceline("# EnableElectrostatic: %d\n", EnableElectrostatic);
     write_traceline("# ThermostatGamma: %f\n", ThermostatGamma);
+    if (SystemParametersFileName != NULL) {
+        write_traceline("# SystemParametersFileName: %s\n", SystemParametersFileName);
+    }
+    if (GromacsOutputBaseName != NULL) {
+        write_traceline("# GromacsOutputBaseName: %s\n", GromacsOutputBaseName);
+    }
     write_traceline("#\n");
 }
 
diff --git a/sim/src/newtables.c b/sim/src/newtables.c
index 950289332..e5abb6644 100755
--- a/sim/src/newtables.c
+++ b/sim/src/newtables.c
@@ -642,6 +642,22 @@ tokenizeDouble(int *errp)
 }
 
 static void
+destroyElement(void *e)
+{
+  struct atomType *element = (struct atomType *)e;
+
+  if (element == NULL || element->refCount-- > 1) {
+    return;
+  }
+
+  free(element->name);
+  element->name = NULL;
+  free(element->symbol);
+  element->symbol = NULL;
+  free(element);
+}
+
+static void
 destroyBondStretch(void *s)
 {
   struct bondStretch *stretch = (struct bondStretch *)s;
@@ -704,6 +720,8 @@ destroyElectrostatic(void *e)
 static void
 destroyStaticBondTable(void)
 {
+  hashtable_destroy(periodicHashtable, destroyElement);
+  periodicHashtable = NULL;
   hashtable_destroy(bondStretchHashtable, destroyBondStretch);
   bondStretchHashtable = NULL;
   hashtable_destroy(bendDataHashtable, destroyBendData);
@@ -964,7 +982,6 @@ initializeStaticBondTable(void)
 
 #include "bonds.gen"
 
-  
   addDeTableEntry("H-1-N",  0.75);
   addDeTableEntry("N-1-O",  0.383);
   addDeTableEntry("N-1-F",  0.422);
@@ -976,12 +993,6 @@ initializeStaticBondTable(void)
   addDeTableEntry("S-1-Cl", 0.489);
 
 #include "bends.gen"
-
-  //                        name       rvdW evdW  start  end
-
-  addVanDerWaalsInteraction("Pl-v-Pl", 7.2, 0.3, 100.0, 7.2);
-  addVanDerWaalsInteraction("Pl-v-Pe", 7.2, 0.3, 100.0, 7.2);
-  addVanDerWaalsInteraction("Pe-v-Pe", 7.2, 0.3, 100.0, 7.2);
 }
 
 static const char bends_rcsid[] = RCSID_BENDS_H;
@@ -1046,7 +1057,7 @@ initializeBondTable(void)
   }
   if (reloadSystemOverlay || reloadUserOverlay) {
     initializeStaticBondTable();
-    
+
     readBondTableOverlay(systemBondTableOverlayFileName);
     readBondTableOverlay(userBondTableOverlayFileName);
   }
diff --git a/sim/src/pam5_patterns.c b/sim/src/pam5_patterns.c
index 66dab7527..56494498c 100644
--- a/sim/src/pam5_patterns.c
+++ b/sim/src/pam5_patterns.c
@@ -2,7 +2,7 @@
 
 #include "simulator.h"
 
-static char const rcsid[] = "$Id:$";
+static char const rcsid[] = "$Id$";
 
 /*
 static struct bendData *pam5_Ax_Ax_Ss_low = NULL;
@@ -232,6 +232,12 @@ createPam5Patterns(void)
   struct compiledPatternTraversal *t[10];
   struct compiledPatternAtom *a[10];
   //struct patternParameter *param;
+
+  if (VanDerWaalsCutoffRadius < 0.0) {
+    // this indicates that the model has no pam5 atoms
+    return;
+  }
+  stack_match_initialized = 0;
   
   /*
   a[0] = makePatternAtom(0, "Ax5");
diff --git a/sim/src/part.c b/sim/src/part.c
index 58fde8a7e..c15948ca0 100755
--- a/sim/src/part.c
+++ b/sim/src/part.c
@@ -469,7 +469,7 @@ makeTorsion(struct part *p, int index, struct bond *center, struct bond *b1, str
     // These numbers are based on a torsion around a Carbon-Carbon bond.
     switch (center->order) {
     case '2':
-        // Barrior to rotation of a simple alkene is about 265 kJ/mol, but
+        // Barrier to rotation of a simple alkene is about 265 kJ/mol, but
         // can be on the order of 50 kJ/mol for "captodative ethylenes",
         // where the charge density on the carbons involved in the double
         // bond has been significantly altered.
@@ -483,7 +483,9 @@ makeTorsion(struct part *p, int index, struct bond *center, struct bond *b1, str
     case 'a':
     case 'g':
         // Damian has calculated the following for a small graphitic system
-        t->A = 0.37013376;
+        //t->A = 0.37013376;
+        t->A = 0.04;
+        //t->A = 0.0;
         break;
     default:
         t->A = 0;
@@ -605,6 +607,7 @@ makeOutOfPlane(struct part *p, int index, struct atom *a)
 
     // A is in aJ/pm^2
     o->A = 0.00025380636; // This is for carbon in graphene with deflection less than 0.5 pm.
+    //o->A = 0.0;
     //o->A = 0.0005; // XXX need to get actual value from real parameters
 }
 
diff --git a/sim/src/printGromacsTopology.c b/sim/src/printGromacsTopology.c
index c0f3d5473..52359a170 100644
--- a/sim/src/printGromacsTopology.c
+++ b/sim/src/printGromacsTopology.c
@@ -90,7 +90,10 @@ writeExclusion(FILE *top,
     return gotOne;
 }
 
-#define DEPTH_TO_EXCLUDE 2
+
+// vdw cutoff radius divided by basepair to basepair distance
+// 11 nm / 318 pm = 34.6, round up and add some fudge
+#define DEPTH_TO_EXCLUDE 40
 
 static void
 writeGromacsExclusions(FILE *top, struct part *p, struct atom *a)
@@ -197,6 +200,8 @@ static char *closure_nonbondedPass1Symbol;
 static int closure_nonbondedPass1Number;
 static struct part *closure_part;
 
+static int nonbonded_function; // 1=Lennard-Jones, 2=Buckingham
+
 static void
 allNonBondedAtomtypesPass2(char *symbol, void *value)
 {
@@ -205,9 +210,9 @@ allNonBondedAtomtypesPass2(char *symbol, void *value)
     struct vanDerWaalsParameters *vdw;
     double rvdW; // nm
     double evdW; // kJ mol^-1
-    double A; // kJ mol^-1
-    double B; // nm^-1
-    double C; // kJ mol^-1 nm^6
+    double A;
+    double B;
+    double C;
     
     if (at != NULL) {
         element = at->protons;
@@ -218,11 +223,18 @@ allNonBondedAtomtypesPass2(char *symbol, void *value)
                 if (rvdW > 1e-8) {
                     evdW = zJ_to_kJpermol(vdw->evdW);
 
-                    A = 2.48e5 * evdW;
-                    B = 12.5 / rvdW;
-                    C = evdW * 1.924 * pow(rvdW, 6.0);
+                    if (nonbonded_function == 1) {
+                        A = 2.0 * evdW * pow(rvdW, 6.0);
+                        B = evdW * pow(rvdW, 12.0);
+
+                        fprintf(closure_topologyFile, "%4s %4s    1 %12.5e %12.5e\n", closure_nonbondedPass1Symbol, symbol, A, B);
+                    } else {
+                        A = 2.48e5 * evdW;                 // kJ mol^-1
+                        B = 12.5 / rvdW;                   // nm^-1
+                        C = evdW * 1.924 * pow(rvdW, 6.0); // kJ mol^-1 nm^6
 
-                    fprintf(closure_topologyFile, "%4s %4s    2 %12.5e %12.5e %12.5e\n", closure_nonbondedPass1Symbol, symbol, A, B, C);
+                        fprintf(closure_topologyFile, "%4s %4s    2 %12.5e %12.5e %12.5e\n", closure_nonbondedPass1Symbol, symbol, A, B, C);
+                    }
                 }
             }
         }
@@ -262,9 +274,10 @@ printGromacsToplogy(char *basename, struct part *p)
     FILE *mdp; // Gromacs configuration file (basename.mdp)
     FILE *ndx; // Gromacs group (index) file (basename.ndx)
     int len;
+    double vdwCutoff;
     char *fileName;
     char *ret = NULL;
-    
+
     len = strlen(basename) + 5;
     fileName = allocate(len);
     sprintf(fileName, "%s.top", basename);
@@ -317,10 +330,22 @@ printGromacsToplogy(char *basename, struct part *p)
     fprintf(mdp, "nstcgsteep          =  100\n"); // frequency of steep steps during cg
     fprintf(mdp, "nstlist             =  10\n"); // update frequency for neighbor list
     fprintf(mdp, "ns_type             =  simple\n"); // neighbor search type, must be simple for pbc=no
+
+    if (VanDerWaalsCutoffRadius < 0) {
+        vdwCutoff = 1.0;
+        nonbonded_function = 2;
+    } else {
+        vdwCutoff = VanDerWaalsCutoffRadius;
+        fprintf(mdp, "coulombtype         =  User\n");
+        fprintf(mdp, "vdwtype             =  User\n");
+        nonbonded_function = 1;
+    }
+
     // rlist, rcoulomb and rvdw must be equal when ns_type = simple
-    fprintf(mdp, "rlist               =  %f\n", VanDerWaalsCutoffRadius); // short range neighbor list cutoff distance
-    fprintf(mdp, "rcoulomb            =  %f\n", VanDerWaalsCutoffRadius); // coulomb function cutoff distance
-    fprintf(mdp, "rvdw                =  %f\n", VanDerWaalsCutoffRadius); // vdw cutoff distance
+    fprintf(mdp, "rlist               =  %f\n", vdwCutoff); // short range neighbor list cutoff distance
+    fprintf(mdp, "rcoulomb            =  %f\n", vdwCutoff); // coulomb function cutoff distance
+    fprintf(mdp, "rvdw                =  %f\n", vdwCutoff); // vdw cutoff distance
+    
     fprintf(mdp, "epsilon_r           =  %f\n", DielectricConstant);
     fprintf(mdp, "freezegrps          =  Anchor\n"); // which group of atoms to hold fixed
     fprintf(mdp, "freezedim           =  Y Y Y\n"); // fix in all three dimensions
@@ -335,7 +360,7 @@ printGromacsToplogy(char *basename, struct part *p)
     
     fprintf(top, "[ defaults ]\n");
     fprintf(top, "; nbfunc        comb-rule       gen-pairs       fudgeLJ fudgeQQ\n");
-    fprintf(top, "  2             1               no              1.0     1.0\n");
+    fprintf(top, "  %d             1               no              1.0     1.0\n", nonbonded_function);
     fprintf(top, "\n");
 
     fprintf(top, "[ atomtypes ]\n");
diff --git a/sim/src/sim-params.txt b/sim/src/sim-params.txt
deleted file mode 100755
index 9a8b9530d..000000000
--- a/sim/src/sim-params.txt
+++ /dev/null
@@ -1,498 +0,0 @@
-#
-# Copyright 2007 Nanorex, Inc.  See LICENSE file for details. 
-# $Id$
-#
-
-# This file should be placed in your ~/Nanorex directory.  It is read
-# by the simulator before each simulation or minimization run.  You
-# should be able to edit and save it between runs and see the new
-# results in later runs.
-
-# The element, stretch, and bend lines define new force field
-# parameters which override or extend the force field compiled into
-# the simulator.
-
-# Angle values can be entered in either degrees or radians.  The units
-# line lets you specify which.  You can switch between the two as often
-# as you like.  The default is:
-#
-#units radians
-
-units degrees
-
-# format for element lines
-#
-#    Z (int)    number of protons, or atomType index
-#  grp (int)    group number in periodic table (not currently used)
-#                 groups 9-22 are lanthanides
-#                 groups 8-31 are transition metals
-#  per (int)    period in periodic table (not currently used)
-#  sym (string) abbreviated symbol name (one-three characters)
-#                 sym values are used in stretch and bend records
-# name (string) full name, for printing
-# mass (double) in yg (yoctograms, or 1e-24 g)
-# rvdW (double) van der Waals radius, in 1e-10 m or angstroms or 0.1 nm
-# evdW (double) van der Waals stiffness, in zJ (zepto Joules, or milli atto Joules, or 1e-21 J)
-#                 NOTE: specifing an evdW value < .1 will cause the value to be calculated based on number of protons
-# rcov (double) covalent radius in pm (1e-12 m)
-#                 used to generate unspecified bond parameters
-# chrg (double) charge in mulitples of proton charge
-#
-#         Z grp per par sym   name                      mass    rvdW  evdW  bnds rcov chrg virt
-
-element 997  0  0   All PAM5  All-PAM5-Pseudo-Atoms       0.0   0.0    0.0   0     0   0    0
-element 996  0  0   PAM5 P5S  PAM5-Sugars                 0.0   0.0    0.0   0     0   0    0
-element 995  0  0   PAM5 P5P  PAM5-Phosphates             0.0   0.0    0.0   0     0   0    0
-element 994  0  0   PAM5 P5G  PAM5-Major-Grooves          0.0   0.0    0.0   0     0   0    0
-element 993  0  0   PAM5 P5V  PAM5-Virtual-Atoms          0.0   0.0    0.0   0     0   0    0
-element 992  0  0   PAM5 P5d  PAM5-depricated             0.0   0.0    0.0   0     0   0    0
-element 991  0  0   All PAM3  All-PAM3-Pseudo-Atoms       0.0   0.0    0.0   0     0   0    0
-
-element 200  0  0   P5d Ax5   DNA-Pseudo-Axis           167.0   0.0    0.0   4   100   0    0   700
-element 201  0  0   P5S Ss5   DNA-Pseudo-Sugar          167.0   0.0    0.0   3   170   0    0   800
-element 202  0  0   P5P Pl5   DNA-Pseudo-Phosphate      167.0   0.0    0.0   2   170   0    0   900
-element 203  0  0   P5d Sj5   DNA-Pseudo-Sugar-Junction 167.0   0.0    0.0   3   170   0    0   810
-element 204  0  0   P5d Ae5   DNA-Pseudo-Axis-End       167.0   0.0    0.0   1   100   0    0   701
-element 205  0  0   P5d Pe5   DNA-Pseudo-Phosphate-End  167.0   0.0    0.0   1   170   0    0   901
-element 206  0  0   P5d Sh5   DNA-Pseudo-Sugar-End      167.0   0.0    0.0   1   170   0    0   902
-element 207  0  0   P5d Hp5   DNA-Pseudo-Hairpin        167.0   0.0    0.0   2   100   0    0   820
-element 208  0  0   P5G Gv5   DNA-Pseudo-Groove         167.0   0.0    0.0   2   100   0    0   820
-element 209  0  0   P5G Gr5   DNA-Pseudo-Groove-End     167.0   0.0    0.0   2   100   0    0   820
-
-element 220  0  0   P5V vDa1  virtual-DNA-planeA-num1     0.0   0.0    0.0   1   100   0    1
-element 221  0  0   P5V vDa2  virtual-DNA-planeA-num2     0.0   0.0    0.0   1   100   0    1
-element 222  0  0   P5V vDa3  virtual-DNA-planeA-num3     0.0   0.0    0.0   1   100   0    1
-element 223  0  0   P5V vDa4  virtual-DNA-planeA-num4     0.0   0.0    0.0   1   100   0    1
-element 224  0  0   P5V vDa5  virtual-DNA-planeA-num5     0.0   0.0    0.0   1   100   0    1
-element 225  0  0   P5V vDa6  virtual-DNA-planeA-num6     0.0   0.0    0.0   1   100   0    1
-element 226  0  0   P5V vDa7  virtual-DNA-planeA-num7     0.0   0.0    0.0   1   100   0    1
-element 227  0  0   P5V vDa8  virtual-DNA-planeA-num8     0.0   0.0    0.0   1   100   0    1
-
-element 230  0  0   P5V vDb1  virtual-DNA-planeB-num1     0.0   0.0    0.0   1   100   0    1
-element 231  0  0   P5V vDb2  virtual-DNA-planeB-num2     0.0   0.0    0.0   1   100   0    1
-element 232  0  0   P5V vDb3  virtual-DNA-planeB-num3     0.0   0.0    0.0   1   100   0    1
-element 233  0  0   P5V vDb4  virtual-DNA-planeB-num4     0.0   0.0    0.0   1   100   0    1
-element 234  0  0   P5V vDb5  virtual-DNA-planeB-num5     0.0   0.0    0.0   1   100   0    1
-element 235  0  0   P5V vDb6  virtual-DNA-planeB-num6     0.0   0.0    0.0   1   100   0    1
-element 236  0  0   P5V vDb7  virtual-DNA-planeB-num7     0.0   0.0    0.0   1   100   0    1
-element 237  0  0   P5V vDb8  virtual-DNA-planeB-num8     0.0   0.0    0.0   1   100   0    1
-
-element 240  0  0   P5V vDn   virtual-DNA-non-bonded      0.0   0.0    0.0   0   100   0    1
-
-element 300  0  0   PAM3 Ax3  PAM3-Axis                 167.0   0.0    0.0   4   100   0    0   700
-element 301  0  0   PAM3 Ss3  PAM3-Sugar                167.0   0.0    0.0   3   170   0    0   800
-element 302  0  0   PAM3 Pl3  PAM3-Phosphate-Link       167.0   3.6   10.0   2   170  -1    0   900
-element 303  0  0   PAM3 Sj3  PAM3-Sugar-Junction       167.0   0.0   10.0   3   170   0    0   810
-element 304  0  0   PAM3 Ae3  PAM3-Axis-End             167.0   0.0    0.0   1   100   0    0   701
-element 305  0  0   PAM3 Se3  PAM3-Sugar-End            167.0   3.6   10.0   1   170  -2    0   901
-element 306  0  0   PAM3 Sh3  PAM3-Sugar-Hydroxyl       167.0   0.0    0.0   1   170   0    0   902
-element 307  0  0   PAM3 Hp3  PAM3-Hairpin              167.0   0.0    0.0   2   100   0    0   820
-
-# format for vdw lines
-#
-# rvdW              (double) van der Waals radius in pm or 1e-12 m
-# evdW              (double) van der Waals energy in zJ or 1e-21 J
-# cutoffRadiusStart (double) start of smooth transition in pm
-# cutoffRadiusEnd   (double) end of smooth transition in pm
-# name              (string) symbol-v-symbol
-#                        The atomType (number of protons) of the first symbol must be <= the second.
-#
-# The vdw potential is multiplied by a smooth transition function
-# between cutoffRadiusStart and cutoffRadiusEnd.  Beyond
-# cutoffRadiusEnd the vdw potential is identically zero.  If
-# cutoffRadiusEnd < cutoffRadiusStart, this transition is disabled,
-# and the potential is shifted so that it is zero at cutoffRadiusEnd.
-# If cutoffRadiusStart < 0, it is set to rvdW.  If cutoffRadiusEnd <
-# 0, it is set to rvdW * VanDerWaalsCutoffFactor (specified by
-# --vdw-cutoff-factor).  Setting cutoffRadiusEnd to rvdW, and
-# cutoffRadiusStart to any larger value selects only the repulsive
-# interaction.
-#
-#  rvdW evdW start end name
-
-vdw 200.0 10.0 100.0 7.2 vDn-v-vDn
-
-vdw 7.2 10.0 100.0 7.2 Pl3-v-Pl3
-vdw 7.2 10.0 100.0 7.2 Pl3-v-Se3
-vdw 7.2 10.0 100.0 7.2 Se3-v-Se3
-
-# format for stretch lines
-#
-#          ks (double) in N/m
-#          r0 (double) equilibrium distance, in pm, or 1e-12 m
-#          de (double) in aJ, or 1e-18 J
-#        beta (double) in 1e10 m^-1
-#                        set to sqrt(ks / (2.0 * de)) / 10.0 if value here is less than zero
-# inflectionR (double) r value in pm where d^2(Lippincott(r)) / dr^2 == 0
-#                        inflectionR is end of interpolation table during minimization
-#                        set to r0*1.5 if value here is less than zero
-#        qual (int)    quality of parameter (use of a parameter with quality < 5 produces a warning)
-#        quad (int)    flag, non-zero if this stretch should be quadratic instead of Lippincott/Morse
-#    bondName (string) symbol-bondOrder-symbol
-#                        bondOrders are: (1, a, g, 2, 3)  a is aromatic, g is graphitic
-#                        The atomType (number of protons) of the first symbol must be <= the second.
-#
-#         ks    r0      de      beta    inflectionR qual quad bondName
-
-stretch   4.00  318.00  1.0000   -1         -1       9    1   Ax5-1-Ax5
-stretch  50.00  676.00  1.0000   -1         -1       9    1   Ax5-1-Ss5
-stretch  50.00  676.00  1.0000   -1         -1       9    1   Ax5-1-Sj5
-stretch   4.00  364.00  1.0000   -1         -1       9    1   Ss5-1-Pl5
-stretch   4.00  400.00  1.0000   -1         -1       9    1   Pl5-1-Sj5
-stretch   4.00  180.00  1.0000   -1         -1       9    1   H-1-Ax5
-stretch   4.00  200.00  1.0000   -1         -1       9    1   H-1-Ss5
-stretch   4.00  200.00  1.0000   -1         -1       9    1   H-1-Pl5
-stretch   4.00  180.00  1.0000   -1         -1       9    1   Ax5-1-Ae5
-stretch   4.00  200.00  1.0000   -1         -1       9    1   Ss5-1-Sh5
-stretch   4.00  364.00  1.0000   -1         -1       9    1   Ss5-1-Pe5
-stretch   4.00  357.00  1.0000   -1         -1       9    1   Pl5-1-Hp5
-stretch   4.00  357.00  1.0000   -1         -1       9    1   Pe5-1-Hp5
-stretch   4.00  200.00  1.0000   -1         -1       9    1   Sh5-1-Hp5
-stretch   4.00  200.00  1.0000   -1         -1       9    1   H-1-Hp5
-
-stretch  50.00 1239.60  1.0000   -1         -1       9    1   Ss5-1-Ss5
-stretch  50.00 1064.70  1.0000   -1         -1       9    1   Gv5-1-Ss5
-stretch  50.00 1064.70  1.0000   -1         -1       9    1   Gr5-1-Ss5
-stretch   0.00  300.00  1.0000   -1         -1       9    1   Gv5-1-Gv5
-stretch   0.00  300.00  1.0000   -1         -1       9    1   Gv5-1-Gr5
-
-
-stretch   4.00  318.00  1.0000   -1         -1       9    1   Ax3-1-Ax3
-stretch   4.00  318.00  1.0000   -1         -1       9    1   Ax3-1-Ae3
-stretch  50.00  870.00  1.0000   -1         -1       9    1   Ax3-1-Ss3
-stretch  50.00  870.00  1.0000   -1         -1       9    1   Ax3-1-Sj3
-stretch  50.00  870.00  1.0000   -1         -1       9    1   Ax3-1-Se3
-stretch   4.00  318.00  1.0000   -1         -1       9    1   Ae3-1-Ax3
-stretch   4.00  318.00  1.0000   -1         -1       9    1   Ae3-1-Ae3
-stretch  50.00  870.00  1.0000   -1         -1       9    1   Ae3-1-Ss3
-stretch  50.00  870.00  1.0000   -1         -1       9    1   Ae3-1-Sj3
-stretch  50.00  870.00  1.0000   -1         -1       9    1   Ae3-1-Se3
-stretch   4.00  400.00  1.0000   -1         -1       9    1   Pl3-1-Sj3
-stretch   4.00  180.00  1.0000   -1         -1       9    1   H-1-Ax3
-stretch   4.00  200.00  1.0000   -1         -1       9    1   H-1-Ss3
-stretch   4.00  200.00  1.0000   -1         -1       9    1   H-1-Pl3
-stretch   4.00  200.00  1.0000   -1         -1       9    1   Ss3-1-Sh3
-stretch   4.00  357.00  1.0000   -1         -1       9    1   Se3-1-Hp3
-stretch  50.00  870.00  1.0000   -1         -1       9    1   Se3-1-Ae3
-stretch   4.00  200.00  1.0000   -1         -1       9    1   Sh3-1-Hp3
-stretch   4.00  200.00  1.0000   -1         -1       9    1   H-1-Hp3
-stretch   4.00  625.00  1.0000   -1         -1       9    1   Ss3-1-Ss3
-stretch   4.00  625.00  1.0000   -1         -1       9    1   Ss3-1-Sj3
-stretch   4.00  625.00  1.0000   -1         -1       9    1   Se3-1-Ss3
-stretch   4.00  625.00  1.0000   -1         -1       9    1   Ss3-1-Se3
-stretch  50.00  870.00  1.0000   -1         -1       9    1   Ss3-1-Ae3
-stretch   4.00  625.00  1.0000   -1         -1       9    1   Se3-1-Sj3
-stretch   4.00  670.00  1.0000   -1         -1       9    1   Sj3-1-Sj3
-
-# format for bend lines
-#
-# ktheta (double) in aJ / rad^2 (1e-18 J/rad^2)
-# theta0 (double) in radians
-#   qual (int)    quality of parameter (use of a parameter with quality < 5 produces a warning)
-#   name (string) symbol-bondOrder-symbol.hybridization-bondOrder-symbol
-#                        bondOrders are: (1, a, g, 2, 3)  a is aromatic, g is graphitic
-#                        atoms in group 3 have a default hybridization of sp2
-#                        other atoms have a default hybridization of sp3
-#                        an info line in the mmp file can change the hybridization
-#                        possible values are: (sp, sp2, sp2_g, sp3, sp3d)
-#                        sp2_g is graphitic, sp3d is not supported yet
-#
-#    ktheta          theta0  qual  bondName
-
-# 180 degree along Axis
-bend   0.18          180.000   9   Ax5-1-Ax5.sp3-1-Ax5
-#bend  0.18          180.000   9   H-1-Ax5.sp3-1-Ax5 #duplicate, H is sugar
-#bend  0.18          180.000   9   H-1-Ax5.sp3-1-Ae5 #duplicate, H is sugar
-bend   0.18          180.000   9   Ax5-1-Ax5.sp3-1-Ae5
-bend   0.18          180.000   9   Ae5-1-Ax5.sp3-1-Ae5
-
-# 90 degree Axis to Sugar
-bend   1.0            90.000   9   Ax5-1-Ax5.sp3-1-Ss5
-bend   1.0            90.000   9   Ax5-1-Ax5.sp3-1-Sj5
-#bend  1.0            90.000   9   H-1-Ax5.sp3-1-Ss5 #duplicate, H is sugar
-bend   1.0            90.000   9   Ss5-1-Ax5.sp3-1-Ae5
-bend   1.0            90.000   9   H-1-Ax5.sp3-1-Ax5
-bend   1.0            90.000   9   H-1-Ax5.sp3-1-Ae5
-bend   1.0            90.000   9   H-1-Ax5.sp3-1-H
-
-# 133 degree minor groove
-bend   1.0           133.000   9   Ss5-1-Ax5.sp3-1-Ss5
-bend   1.0           133.000   9   Ss5-1-Ax5.sp3-1-Sj5
-bend   1.0           133.000   9   Sj5-1-Ax5.sp3-1-Sj5
-bend   1.0           133.000   9   H-1-Ax5.sp3-1-Ss5
-bend   1.0           133.000   9   H-1-Ax5.sp3-1-Sj5
-
-# 121 degree Axis Sugar Phosphate
-bend   0.04          121.000   9   Ax5-1-Ss5.sp3-1-Pl5
-bend   0.04          121.000   9   Ax5-1-Ss5.sp3-1-Pe5
-bend   0.04          121.000   9   Ax5-1-Ss5.sp3-1-Sh5
-bend   0.04          121.000   9   H-1-Ss5.sp3-1-Ax5
-
-# 127 degree Phosphate Sugar Phosphate
-bend   0.04          127.000   9   Pl5-1-Ss5.sp3-1-Pl5
-bend   0.04          127.000   9   Pl5-1-Ss5.sp3-1-Pe5
-bend   0.04          127.000   9   Pl5-1-Ss5.sp3-1-Sh5
-bend   0.04          127.000   9   Pe5-1-Ss5.sp3-1-Pe5
-bend   0.04          127.000   9   Pe5-1-Ss5.sp3-1-Sh5
-bend   0.04          127.000   9   Sh5-1-Ss5.sp3-1-Sh5
-bend   0.04          127.000   9   H-1-Ss5.sp3-1-Pl5
-bend   0.04          127.000   9   H-1-Ss5.sp3-1-Pe5
-bend   0.04          127.000   9   H-1-Ss5.sp3-1-Sh5
-bend   0.04          127.000   9   H-1-Ss5.sp3-1-H
-
-# 127 degree Phosphate Hairpin Phosphate
-bend   0.04          127.000   9   Pl5-1-Hp5.sp3-1-Pl5
-bend   0.04          127.000   9   Pl5-1-Hp5.sp3-1-Pe5
-bend   0.04          127.000   9   Pl5-1-Hp5.sp3-1-Sh5
-bend   0.04          127.000   9   Pe5-1-Hp5.sp3-1-Pe5
-bend   0.04          127.000   9   Pe5-1-Hp5.sp3-1-Sh5
-bend   0.04          127.000   9   Sh5-1-Hp5.sp3-1-Sh5
-bend   0.04          127.000   9   H-1-Hp5.sp3-1-Pl5
-bend   0.04          127.000   9   H-1-Hp5.sp3-1-Pe5
-bend   0.04          127.000   9   H-1-Hp5.sp3-1-Sh5
-bend   0.04          127.000   9   H-1-Hp5.sp3-1-H
-
-# 115 degree Axis JunctionSugar Phosphate
-bend   0.04          115.000   9   Ax5-1-Sj5.sp3-1-Pl5
-bend   0.04          115.000   9   Ax5-1-Sj5.sp3-1-Pe5
-bend   0.04          115.000   9   Ax5-1-Sj5.sp3-1-Sh5
-bend   0.04          115.000   9   H-1-Sj5.sp3-1-Ax5
-
-# 110 degree Phosphate JunctionSugar Phosphate
-bend   0.04          110.000   9   Pl5-1-Sj5.sp3-1-Pl5
-bend   0.04          110.000   9   Pl5-1-Sj5.sp3-1-Pe5
-bend   0.04          110.000   9   H-1-Sj5.sp3-1-Pl5
-bend   0.04          110.000   9   H-1-Sj5.sp3-1-H
-bend   0.04          110.000   9   H-1-Sj5.sp3-1-Pe5
-bend   0.04          110.000   9   Pe5-1-Sj5.sp3-1-Pe5
-
-# 127 degree Phosphate JunctionSugar end
-bend   0.04          127.000   9   Pl5-1-Sj5.sp3-1-Sh5
-bend   0.04          127.000   9   Pe5-1-Sj5.sp3-1-Sh5
-bend   0.04          127.000   9   Sh5-1-Sj5.sp3-1-Sh5
-bend   0.04          127.000   9   H-1-Sj5.sp3-1-Sh5
-
-# 92.5 degree Sugar Phosphate Sugar
-bend   0.04           92.500   9   Ss5-1-Pl5.sp3-1-Ss5
-bend   0.04           92.500   9   Ss5-1-Pl5.sp3-1-Sh5
-bend   0.04           92.500   9   Ss5-1-Pl5.sp3-1-Hp5
-bend   0.04           92.500   9   Sh5-1-Pl5.sp3-1-Sh5
-bend   0.04           92.500   9   Sh5-1-Pl5.sp3-1-Hp5
-bend   0.04           92.500   9   Hp5-1-Pl5.sp3-1-Hp5
-bend   0.04           92.500   9   H-1-Pl5.sp3-1-Ss5
-bend   0.04           92.500   9   H-1-Pl5.sp3-1-Sh5
-bend   0.04           92.500   9   H-1-Pl5.sp3-1-Hp5
-bend   0.04           92.500   9   H-1-Pl5.sp3-1-H
-
-# 92.5 degree Sugar Phosphate JunctionSugar
-bend   0.04           92.500   9   Ss5-1-Pl5.sp3-1-Sj5
-bend   0.04           92.500   9   Sj5-1-Pl5.sp3-1-Sh5
-bend   0.04           92.500   9   Sj5-1-Pl5.sp3-1-Hp5
-bend   0.04           92.500   9   H-1-Pl5.sp3-1-Sj5
-
-# 115.8 degree JunctionSugar Phosphate JunctionSugar
-bend   0.04          115.800   9   Sj5-1-Pl5.sp3-1-Sj5
-
-# PAM3 Bend Parameters ####################################3
-
-# 180 degree along Axis
-bend   0.18          180.000   9   Ax3-1-Ax3.sp3-1-Ax3
-#bend  0.18          180.000   9   H-1-Ax3.sp3-1-Ax3 #duplicate, H is sugar
-#bend  0.18          180.000   9   H-1-Ax3.sp3-1-Ae3 #duplicate, H is sugar
-bend   0.18          180.000   9   Ax3-1-Ax3.sp3-1-Ae3
-bend   0.18          180.000   9   Ae3-1-Ax3.sp3-1-Ae3
-
-# 90 degree Axis to Sugar
-bend   1.0            90.000   9   Ax3-1-Ax3.sp3-1-Ss3
-bend   1.0            90.000   9   Ax3-1-Ax3.sp3-1-Sj3
-bend   1.0            90.000   9   Ax3-1-Ax3.sp3-1-Se3
-bend   1.0            90.000   9   Ax3-1-Ae3.sp3-1-Ss3
-bend   1.0            90.000   9   Ax3-1-Ae3.sp3-1-Sj3
-bend   1.0            90.000   9   Ax3-1-Ae3.sp3-1-Se3
-bend   1.0            90.000   9   Ss3-1-Ax3.sp3-1-Ae3
-bend   1.0            90.000   9   Sj3-1-Ax3.sp3-1-Ae3
-bend   1.0            90.000   9   Ss3-1-Ae3.sp3-1-Ae3
-bend   1.0            90.000   9   Sj3-1-Ae3.sp3-1-Ae3
-bend   1.0            90.000   9   Ae3-1-Ax3.sp3-1-Se3
-bend   1.0            90.000   9   Ae3-1-Ae3.sp3-1-Se3
-#bend  1.0            90.000   9   H-1-Ax3.sp3-1-Ss3 #duplicate, H is sugar
-#bend  1.0            90.000   9   H-1-Ax3.sp3-1-Sj3 #duplicate, H is sugar
-#bend  1.0            90.000   9   H-1-Ax3.sp3-1-Se3 #duplicate, H is sugar
-bend   1.0            90.000   9   H-1-Ax3.sp3-1-Ax3
-bend   1.0            90.000   9   H-1-Ax3.sp3-1-Ae3
-bend   1.0            90.000   9   H-1-Ax3.sp3-1-H
-#bend  1.0            90.000   9   H-1-Ae3.sp3-1-Ss3 #duplicate, H is sugar
-#bend  1.0            90.000   9   H-1-Ae3.sp3-1-Sj3 #duplicate, H is sugar
-#bend  1.0            90.000   9   H-1-Ae3.sp3-1-Se3 #duplicate, H is sugar
-bend   1.0            90.000   9   H-1-Ae3.sp3-1-Ax3
-bend   1.0            90.000   9   H-1-Ae3.sp3-1-Ae3
-bend   1.0            90.000   9   H-1-Ae3.sp3-1-H
-
-# 133 degree minor groove
-bend   1.0           133.000   9   Ss3-1-Ax3.sp3-1-Ss3
-bend   1.0           133.000   9   Ss3-1-Ax3.sp3-1-Sj3
-bend   1.0           133.000   9   Ss3-1-Ax3.sp3-1-Se3
-bend   1.0           133.000   9   Sj3-1-Ax3.sp3-1-Sj3
-bend   1.0           133.000   9   H-1-Ax3.sp3-1-Ss3
-bend   1.0           133.000   9   H-1-Ax3.sp3-1-Sj3
-bend   1.0           133.000   9   H-1-Ax3.sp3-1-Se3
-bend   1.0           133.000   9   Ss3-1-Ae3.sp3-1-Ss3
-bend   1.0           133.000   9   Ss3-1-Ae3.sp3-1-Sj3
-bend   1.0           133.000   9   Ss3-1-Ae3.sp3-1-Se3
-bend   1.0           133.000   9   Sj3-1-Ae3.sp3-1-Sj3
-bend   1.0           133.000   9   H-1-Ae3.sp3-1-Ss3
-bend   1.0           133.000   9   H-1-Ae3.sp3-1-Sj3
-bend   1.0           133.000   9   H-1-Ae3.sp3-1-Se3
-
-# 74.58 degree Axis Sugar Sugar
-bend   0.04           74.580   9   Ax3-1-Ss3.sp3-1-Ss3
-bend   0.04           74.580   9   Ax3-1-Ss3.sp3-1-Se3
-bend   0.04           74.580   9   Ax3-1-Ss3.sp3-1-Sh3
-bend   0.04           74.580   9   H-1-Ss3.sp3-1-Ax3
-
-# 74.58 degree Axis-end Sugar Sugar
-bend   0.04           74.580   9   Ss3-1-Se3.sp3-1-Ae3
-bend   0.04           74.580   9   Ss3-1-Ss3.sp3-1-Ae3
-bend   0.04           74.580   9   Ae3-1-Ss3.sp3-1-Sh3
-bend   0.04           74.580   9   Ae3-1-Ss3.sp3-1-Se3
-bend   0.04           74.580   9   H-1-Ss3.sp3-1-Ae3
-
-# 108 degree for Axis JunctionSugar JunctionSugar
-bend   0.04          108.000   9   Ax3-1-Sj3.sp3-1-Sj3
-bend   0.04          108.000   9   Ae3-1-Sj3.sp3-1-Sj3
-
-# 149 degree Sugar Sugar Sugar
-bend   0.04          149.000   9   Ss3-1-Ss3.sp3-1-Ss3
-bend   0.04          149.000   9   Ss3-1-Ss3.sp3-1-Sj3
-bend   0.04          149.000   9   Ss3-1-Ss3.sp3-1-Se3
-bend   0.04          149.000   9   Ss3-1-Ss3.sp3-1-Sh3
-bend   0.04          149.000   9   Se3-1-Ss3.sp3-1-Se3
-bend   0.04          149.000   9   Se3-1-Ss3.sp3-1-Sh3
-bend   0.04          149.000   9   Sh3-1-Ss3.sp3-1-Sh3
-bend   0.04          149.000   9   H-1-Ss3.sp3-1-Ss3
-bend   0.04          149.000   9   H-1-Ss3.sp3-1-Sj3
-bend   0.04          149.000   9   H-1-Ss3.sp3-1-Se3
-bend   0.04          149.000   9   H-1-Ss3.sp3-1-Sh3
-bend   0.04          149.000   9   H-1-Ss3.sp3-1-H
-
-# 149 degree for Sugar JunctionSugar JunctionSugar
-bend   0.04          149.000   9   Ss3-1-Sj3.sp3-1-Sj3
-
-# 74.58 degree Axis JunctionSugar Sugar
-bend   0.04           74.580   9   Ax3-1-Sj3.sp3-1-Ss3
-bend   0.04           74.580   9   Ax3-1-Sj3.sp3-1-Se3
-bend   0.04           74.580   9   Ax3-1-Sj3.sp3-1-Sh3
-bend   0.04           74.580   9   H-1-Sj3.sp3-1-Ax3
-
-# 74.58 degree Axis-end JunctionSugar Sugar
-bend   0.04           74.580   9   Ae3-1-Sj3.sp3-1-Ss3
-bend   0.04           74.580   9   Ae3-1-Sj3.sp3-1-Se3
-bend   0.04           74.580   9   Ae3-1-Sj3.sp3-1-Sh3
-bend   0.04           74.580   9   H-1-Sj3.sp3-1-Ae3
-
-# 150 degree Sugar JunctionSugar Sugar
-bend   0.04          150.000    9   Ss3-1-Sj3.sp3-1-Ss3
-bend   0.04          150.000    9   H-1-Sj3.sp3-1-H
-
-# 150 degree Sugar JunctionSugar end (CHECK/FIX ANGLE)
-bend   0.04          150.000    9   Ss3-1-Sj3.sp3-1-Se3
-bend   0.04          150.000    9   Ss3-1-Sj3.sp3-1-Sh3
-bend   0.04          150.000    9   H-1-Sj3.sp3-1-Se3
-bend   0.04          150.000    9   H-1-Sj3.sp3-1-Sh3
-
-# 115.8 degree JunctionSugar Phosphate-link JunctionSugar
-bend   0.04          115.800    9   Sj3-1-Pl3.sp3-1-Sj3
-
-# 127 degree Sugar Hairpin Sugar (CHECK/FIX ANGLE)
-bend   0.04          127.000    9   Se3-1-Hp3.sp3-1-Se3
-bend   0.04          127.000    9   Se3-1-Hp3.sp3-1-Sh3
-bend   0.04          127.000    9   Sh3-1-Hp3.sp3-1-Sh3
-bend   0.04          127.000    9   H-1-Hp3.sp3-1-Se3
-bend   0.04          127.000    9   H-1-Hp3.sp3-1-Sh3
-bend   0.04          127.000    9   H-1-Hp3.sp3-1-H
-
-# parameters for pattern match routines
-
-pattern PAM5:Ax-Ax-Ss_low_ktheta     1.0
-pattern PAM5:Ax-Ax-Ss_low_theta0     85.000
-
-pattern PAM5:Ax-Ax-Ss_high_ktheta    1.0
-pattern PAM5:Ax-Ax-Ss_high_theta0    95.000
-
-
-# For the PAM5-Stack pattern, two base pair planes are defined, each by
-# a pair of basis vectors from an Ax to an Ss pseudo-atom.  Since the
-# double helix can be viewed from either end (180 degree rotational
-# symmetry), each Ss is similar to the one diagonally opposite it,
-# across the minor groove.  Between the two stacked base pairs, the
-# minor groove rotates, so that one pair of similar Ss pseudo-atoms
-# will always be farther apart than the other.  The farther apart pair
-# we will call P, with the closer pair called Q.
-
-# One base pair is called A, the other B.  Each plane contains a set
-# of numbered virtual interaction sites, so vDa1 is the first site in
-# plane A.  The location of each site is defined as a linear
-# combination of the two basis vectors for that plane, with the basis
-# vectors labeled P and Q, corrosponding to the Ss at the tip of that
-# vector (the Ax is the tail for both).
-
-pattern PAM5-Stack:vDa1-p             0.011
-pattern PAM5-Stack:vDa1-q             0.012
-
-pattern PAM5-Stack:vDb1-p             0.111
-pattern PAM5-Stack:vDb1-q             0.112
-
-pattern PAM5-Stack:vDa2-p             0.021
-pattern PAM5-Stack:vDa2-q             0.022
-
-pattern PAM5-Stack:vDb2-p             0.121
-pattern PAM5-Stack:vDb2-q             0.122
-
-pattern PAM5-Stack:vDa3-p             0.031
-pattern PAM5-Stack:vDa3-q             0.032
-
-pattern PAM5-Stack:vDb3-p             0.131
-pattern PAM5-Stack:vDb3-q             0.132
-
-pattern PAM5-Stack:vDa4-p             0.041
-pattern PAM5-Stack:vDa4-q             0.042
-
-pattern PAM5-Stack:vDb4-p             0.141
-pattern PAM5-Stack:vDb4-q             0.142
-
-pattern PAM5-Stack:vDa5-p             0.051
-pattern PAM5-Stack:vDa5-q             0.052
-
-pattern PAM5-Stack:vDb5-p             0.151
-pattern PAM5-Stack:vDb5-q             0.152
-
-pattern PAM5-Stack:vDa6-p             0.061
-pattern PAM5-Stack:vDa6-q             0.062
-
-pattern PAM5-Stack:vDb6-p             0.161
-pattern PAM5-Stack:vDb6-q             0.162
-
-pattern PAM5-Stack:vDa7-p             0.071
-pattern PAM5-Stack:vDa7-q             0.072
-
-pattern PAM5-Stack:vDb7-p             0.171
-pattern PAM5-Stack:vDb7-q             0.172
-
-pattern PAM5-Stack:vDa8-p             0.081
-pattern PAM5-Stack:vDa8-q             0.082
-
-pattern PAM5-Stack:vDb8-p             0.181
-pattern PAM5-Stack:vDb8-q             0.182
-
-pattern PAM5-Stack:vDn-pq             0.250
-
-#         ks    r0      de      beta    inflectionR qual quad bondName
-
-stretch   1.00  300.00  1.0000   -1         -1       9    1   vDa1-1-vDb1
-stretch   1.00  300.00  1.0000   -1         -1       9    1   vDa2-1-vDb2
-stretch   1.00  300.00  1.0000   -1         -1       9    1   vDa3-1-vDb3
-stretch   1.00  300.00  1.0000   -1         -1       9    1   vDa4-1-vDb4
-stretch   1.00  300.00  1.0000   -1         -1       9    1   vDa5-1-vDb5
-stretch   1.00  300.00  1.0000   -1         -1       9    1   vDa6-1-vDb6
-stretch   1.00  300.00  1.0000   -1         -1       9    1   vDa7-1-vDb7
-stretch   1.00  300.00  1.0000   -1         -1       9    1   vDa8-1-vDb8
diff --git a/sim/src/sim.pyx b/sim/src/sim.pyx
index 0574fe7b4..d3f212019 100755
--- a/sim/src/sim.pyx
+++ b/sim/src/sim.pyx
@@ -60,13 +60,13 @@ cdef extern from "simhelp.c":
     double Dmass
     double Temperature
     # end of globals.c stuff
-    char *errString
 
     setWriteTraceCallbackFunc(PyObject)
     setFrameCallbackFunc(PyObject)
     getFrame_c()
-    initsimhelp()
+    pyrexInitBondTable()
     void dumpPart()
+    void reinit_globals()
     everythingElse()
     everythingDone()
     cdef char *structCompareHelp()
@@ -74,7 +74,6 @@ cdef extern from "simhelp.c":
     void strcpy(char *, char *) #bruce 051230 guess
 
     void reinitSimGlobals(PyObject)
-    verifySimObject(PyObject)
     specialExceptionIs(PyObject)
 
     #void dynamicsMovie_start()
@@ -95,7 +94,7 @@ class SimulatorInterrupted(Exception):
 
 specialExceptionIs(SimulatorInterrupted)
 
-cdef class BaseSimulator:
+cdef class _Simulator:
     """Pyrex permits access to doc strings"""
 
     # cdef double *data
@@ -108,7 +107,6 @@ cdef class BaseSimulator:
     # except for the issue of the globals not being reset to their initial values.
     
     def __getattr__(self, char *key):
-        verifySimObject(self)
         if key.startswith('_'):
             # important optimization (when Python asks for __xxx__) [bruce 060102]
             raise AttributeError, key
@@ -163,7 +161,12 @@ cdef class BaseSimulator:
                 # probably it would, but this is better anyway
                 return ""
             return BaseFileName
-        elif strcmp(key, "OutFileName") == 0:
+        elif strcmp(key, "InputFileName") == 0:
+            if InputFileName == NULL:
+                # should we raise an AttributeError here?
+                return ""
+            return InputFileName
+        elif strcmp(key, "OutputFileName") == 0:
             if OutputFileName == NULL:
                 # should we raise an AttributeError here?
                 return ""
@@ -200,7 +203,6 @@ cdef class BaseSimulator:
             raise AttributeError, key
 
     def __setattr__(self, char *key, value):
-        verifySimObject(self)
         if strcmp(key, "debug_flags") == 0:
             global debug_flags
             debug_flags = value
@@ -270,7 +272,10 @@ cdef class BaseSimulator:
         elif strcmp(key, "baseFilename") == 0:
             global BaseFileName
             BaseFileName = value
-        elif strcmp(key, "OutFileName") == 0:
+        elif strcmp(key, "InputFileName") == 0:
+            global InputFileName
+            InputFileName = value
+        elif strcmp(key, "OutputFileName") == 0:
             global OutputFileName
             OutputFileName = value
         elif strcmp(key, "TraceFileName") == 0:
@@ -308,7 +313,6 @@ cdef class BaseSimulator:
         # and reraise that exception or some other one from this method
         #bruce 060103
 
-        verifySimObject(self)
         setFrameCallbackFunc(frame_callback)
         setWriteTraceCallbackFunc(trace_callback)
         srand(0)
@@ -320,96 +324,81 @@ cdef class BaseSimulator:
         return
 
     def structCompare(self):
-        verifySimObject(self)
         r = structCompare()
         if r:
             raise Exception, r
 
-class Minimize(BaseSimulator):
-    def __init__(self, fname):
-        global InputFileName
-        reinitSimGlobals(self)
-        self.ToMinimize = 1
-        self.DumpAsText = 1
-        self.PrintFrameNums = 0
-        InputFileName = fname
-        initsimhelp()
-
-class Dynamics(BaseSimulator): #bruce 060101 changed superclass from Minimize to BaseSimulator
-    def __init__(self, fname):
-        global InputFileName
-        reinitSimGlobals(self)
-        self.ToMinimize = 0
-        self.DumpAsText = 0
-        self.PrintFrameNums = 0
-        InputFileName = fname
-        initsimhelp()
-
-def setErrorString(str):
-    errString = str
-
-def getEquilibriumDistanceForBond(element1, element2, order):
-    # element1 and element2 are python ints
-    # order is a python string
-    cdef int int_el1, int_el2
-    cdef char *c_order
-    int_el1 = element1
-    int_el2 = element2
-    c_order = order
-    # initializeBondTable should not require a tracefile, so can be called
-    # at any time.  It must have been called before either parsing an mmp
-    # file, or calling getBondEquilibriumDistance().  It checks to see if
-    # it's been called already, so it's cheap if that's the case.  It
-    # shouldn't affect the saved warning flags in any way.  Warnings are
-    # only printed when bond information is retrieved, and
-    # getBondEquilibriumDistance() avoids the warning code.
-    initializeBondTable()
-    return getBondEquilibriumDistance(int_el1, int_el2, c_order[0])
-
-#####################################################
-# Per-frame callbacks to Python, wware 060101
-
-def getFrame():
-    frm = getFrame_c()
-    num_atoms = len(frm) / (3 * 8)
-    array = Numeric.fromstring(frm, Numeric.Float64)
-    return Numeric.resize(array, [num_atoms, 3])
-
-#  #  #  #  #  #  #  #  #  #  #  #  #  #  #  #  #  #
+    def reinitGlobals(self):
+        reinit_globals()
+
+    def getEquilibriumDistanceForBond(self, element1, element2, order):
+        # element1 and element2 are python ints
+        # order is a python string
+        cdef int int_el1, int_el2
+        cdef char *c_order
+        int_el1 = element1
+        int_el2 = element2
+        c_order = order
+        # initializeBondTable should not require a tracefile, so can be called
+        # at any time.  It must have been called before either parsing an mmp
+        # file, or calling getBondEquilibriumDistance().  It checks to see if
+        # it's been called already, so it's cheap if that's the case.  It
+        # shouldn't affect the saved warning flags in any way.  Warnings are
+        # only printed when bond information is retrieved, and
+        # getBondEquilibriumDistance() avoids the warning code.
+        pyrexInitBondTable()
+        return getBondEquilibriumDistance(int_el1, int_el2, c_order[0])
+
+    def getFrame(self):
+        frm = getFrame_c()
+        num_atoms = len(frm) / (3 * 8)
+        array = Numeric.fromstring(frm, Numeric.Float64)
+        return Numeric.resize(array, [num_atoms, 3])
+
+_theSimulator = None
+
+def theSimulator():
+    global _theSimulator
+    if (_theSimulator is None):
+        _theSimulator = _Simulator()
+    return _theSimulator
+
+#####################################################################################
+# Test code below this point
 
 # conventional globals for callback -- they don't have to be used
-frameNumber = 0
-frameFreq = 1
+_frameNumber = 0
+_frameFreq = 1
 
-callbackCounter = 0
+_callbackCounter = 0
 
-def myCallback(last_frame):
-    global frameNumber
-    frameNumber = frameNumber + 1
-    if (frameNumber % frameFreq) == 0:
-        #print "frame %d:" % frameNumber, getFrame()
-        global callbackCounter
-        callbackCounter = callbackCounter + 1
+def _myCallback(last_frame):
+    global _frameNumber
+    _frameNumber = _frameNumber + 1
+    if (_frameNumber % _frameFreq) == 0:
+        #print "frame %d:" % _frameNumber, getFrame()
+        global _callbackCounter
+        _callbackCounter = _callbackCounter + 1
 
 #bruce 060101 made testsetup a function so it only happens when asked for,
 # not on every import and sim run (for example, runSim.py doesn't want it)
 
-def testsetup(freq=1): 
+def _testsetup(freq=1): 
     "conventional setup for test functions; returns frame_callback argument for .go method"
-    global frameNumber, frameFreq, callbackCounter
-    callbackCounter = 0
-    frameNumber = 0
-    frameFreq = max(1, freq)
-    return myCallback
-
-tracefile = [ ]
-
-def tracecallback(str):
-    global tracefile
-    tracefile.append(str)
-def badcallback(str):
+    global _frameNumber, _frameFreq, _callbackCounter
+    _callbackCounter = 0
+    _frameNumber = 0
+    _frameFreq = max(1, freq)
+    return _myCallback
+
+_tracefile = [ ]
+
+def _tracecallback(str):
+    global _tracefile
+    _tracefile.append(str)
+def _badcallback(str):
     raise RuntimeError, "This is a bad callback"
-def badcallback2():
+def _badcallback2():
     "This callback should really take an argument"
     pass
 
@@ -429,45 +418,68 @@ def isFileAscii(filename):
 class Tests(unittest.TestCase):
 
     def setUp(self):
-        global tracefile
-        tracefile = [ ]
+        global _tracefile
+        _tracefile = [ ]
 
     def test_getEquilibriumDistance(self):
         # try C-C single bond; prints 154.88
         assert (getEquilibriumDistanceForBond(6, 6, '1') - 154.88) ** 2 < 0.1
 
     def test_framecallback(self):
-        func = testsetup(2)
-        m = Minimize("tests/minimize/test_h2.mmp")
+        func = _testsetup(2)
+        m = theSimulator()
+
+        m.reinitGlobals()
+        m.InputFileName = "tests/minimize/test_h2.mmp"
+        m.OutputFileName = "tests/minimize/test_h2.xyz"
+        m.ToMinimize = 1
+        m.DumpAsText = 1
+        m.OutputFormat = 0
+
         m.go(frame_callback=func)
-        assert callbackCounter == 3, "Callback counter is %d, not 3" %(callbackCounter)
+        assert _callbackCounter == 3, "Callback counter is %d, not 3" %(_callbackCounter)
 
     def test_frameAndTraceCallback(self):
-        func = testsetup(10)
-        d = Dynamics("tests/rigid_organics/test_C6H10.mmp")
-        d.go(frame_callback=func, trace_callback=tracecallback)
-        assert callbackCounter == 10
+        func = _testsetup(10)
+        d = theSimulator()
+
+        d.reinitGlobals()
+        d.InputFileName = "tests/rigid_organics/test_C6H10.mmp"
+        d.OutputFileName = "tests/rigid_organics/test_C6H10.dpb"
+        d.ToMinimize = 0
+        d.DumpAsText = 0
+        d.OutputFormat = 1
+
+        d.go(frame_callback=func, trace_callback=_tracecallback)
+        assert _callbackCounter == 10
 
     def test_traceCallbackWithMotor(self):
-        d = Dynamics("tests/dynamics/test_0001.mmp")
-        d.go(trace_callback=tracecallback)
+        d = theSimulator()
+
+        d.reinitGlobals()
+        d.InputFileName = "tests/dynamics/test_0001.mmp"
+        d.OutputFileName = "tests/dynamics/test_0001.dpb"
+        d.ToMinimize = 0
+        d.DumpAsText = 0
+        d.OutputFormat = 1
+
+        d.go(trace_callback=_tracecallback)
         # Make sure there is motor information being printed
-        assert len(tracefile[-5].split()) == 3, \
-               "Motor info not appearing in trace file:" + tracefile[18]
+        assert len(_tracefile[-5].split()) == 3, \
+               "Motor info not appearing in trace file:" + _tracefile[18]
 
     def test_dpbFileShouldBeBinary(self):
-        d = Dynamics("tests/dynamics/test_0001.mmp")
-        d.go()
-        # Make sure that the DPB file is really binary
-        assert not isFileAscii("tests/dynamics/test_0001.dpb")
+        d = theSimulator()
+
+        d.reinitGlobals()
+        d.InputFileName = "tests/dynamics/test_0001.mmp"
+        d.OutputFileName = "tests/dynamics/test_0001.dpb"
+        d.ToMinimize = 0
+        d.DumpAsText = 0
+        d.OutputFormat = 1
 
-    def test_dpbFileShouldBeBinaryAfterMinimize(self):
-        # bruce 060103 added this; it presently fails, but I hope to fix it in same commit
-        m = Minimize("tests/minimize/test_h2.mmp")
-        m.go()
-        d = Dynamics("tests/dynamics/test_0001.mmp")
         d.go()
-        # Make sure that the DPB file is really binary, even after Minimize is run
+        # Make sure that the DPB file is really binary
         assert not isFileAscii("tests/dynamics/test_0001.dpb")
 
 ##     def test_dynamicsStepStuff(self):
@@ -487,37 +499,52 @@ class Tests(unittest.TestCase):
 
     def test_badCallback1(self):
         try:
-            d = Dynamics("tests/dynamics/test_0001.mmp")
-            d.go(trace_callback=badcallback)
+            d = theSimulator()
+
+            d.reinitGlobals()
+            d.InputFileName = "tests/dynamics/test_0001.mmp"
+            d.OutputFileName = "tests/dynamics/test_0001.dpb"
+            d.ToMinimize = 0
+            d.DumpAsText = 0
+            d.OutputFormat = 1
+
+            d.go(trace_callback=_badcallback)
             assert False, "This test should have failed"
         except RuntimeError, e:
             assert e.args[0] == "This is a bad callback"
 
     def test_badCallback2(self):
         try:
-            d = Dynamics("tests/dynamics/test_0001.mmp")
-            d.go(trace_callback=badcallback2)
+            d = theSimulator()
+
+            d.reinitGlobals()
+            d.InputFileName = "tests/dynamics/test_0001.mmp"
+            d.OutputFileName = "tests/dynamics/test_0001.dpb"
+            d.ToMinimize = 0
+            d.DumpAsText = 0
+            d.OutputFormat = 1
+
+            d.go(trace_callback=_badcallback2)
             assert False, "This test should have failed"
         except TypeError:
             pass
 
     def test_badCallback3(self):
         try:
-            d = Dynamics("tests/dynamics/test_0001.mmp")
+            d = theSimulator()
+
+            d.reinitGlobals()
+            d.InputFileName = "tests/dynamics/test_0001.mmp"
+            d.OutputFileName = "tests/dynamics/test_0001.dpb"
+            d.ToMinimize = 0
+            d.DumpAsText = 0
+            d.OutputFormat = 1
+
             d.go(trace_callback=42)
             assert False, "This test should have failed"
         except RuntimeError, e:
             assert e.args[0] == "callback is not callable"
 
-    def test_callWrongSimulatorObject(self):
-        try:
-            m = Minimize("tests/dynamics/test_0001.mmp")
-            d = Dynamics("tests/dynamics/test_0001.mmp")
-            m.go(trace_callback=42)
-            assert False, "This test should have failed"
-        except AssertionError, e:
-            assert e.args[0] == "not the most recent simulator object"
-
 #
 # make pyx && python -c "import sim; sim.test()"
 #
diff --git a/sim/src/simhelp.c b/sim/src/simhelp.c
index b51963bf2..a1442b475 100755
--- a/sim/src/simhelp.c
+++ b/sim/src/simhelp.c
@@ -47,8 +47,6 @@ static struct xyz *pos;
 static char buf[1024];
 static int callback_exception = 0;
 
-static void *mostRecentSimObject = NULL;
-
 // Python exception stuff, wware 010609
 char *py_exc_str = NULL;
 static char py_exc_strbuf[1024];
@@ -151,27 +149,6 @@ finish_python_call(PyObject *retval)
     return retval;
 }
 
-static void
-reinitSimGlobals(PyObject *sim)
-{
-    reinit_globals();
-    mostRecentSimObject = sim;
-}
-
-static PyObject *
-verifySimObject(PyObject *sim)
-{
-    start_python_call();
-    if (sim != mostRecentSimObject) {
-	raiseExceptionIfNoneEarlier(PyExc_AssertionError,
-				    "not the most recent simulator object");
-	WHERE_ARE_WE();
-	return NULL;
-    }
-    WHERE_ARE_WE();
-    return finish_python_call(Py_None);
-}
-
 static PyObject *writeTraceCallbackFunc = NULL;
 static PyObject *frameCallbackFunc = NULL;
 
@@ -328,12 +305,8 @@ getFrame_c(void)
     return finish_python_call(retval);
 }
 
-/*
- * A good goal would be to eliminate all the filename-twiddling in this
- * function, and only set up the bond tables.
- */
 static PyObject *
-initsimhelp(void) // WARNING: this duplicates some code from simulator.c
+pyrexInitBondTable(void)
 {
 #ifdef WWDEBUG
     debug_flags |= D_PYREX_SIM;
@@ -341,26 +314,8 @@ initsimhelp(void) // WARNING: this duplicates some code from simulator.c
 
     start_python_call();
 
-    if (DumpAsText) {
-        OutputFormat = 0;
-    } else {
-        // bruce 060103 part of bugfix for Dynamics output format after Minimize
-        // (to complete the fix it would be necessary for every change by sim.pyx of either
-        //  OutputFormat or DumpAsText to make sure the other one changed to fit,
-        //  either at the time of the change or before the next .go method
-        // (or if changed during that method, before their next use by any C code);
-        // this is not needed by the present client code, so I'll put it off for now
-        // and hope we can more extensively clean up this option later.)
-        OutputFormat = 1; // sim.pyx only tries to support "old" dpb format for now
-    }
-    InputFileName = copy_string(InputFileName);
-    OutputFileName = replaceExtension(InputFileName, DumpAsText ? "xyz" : "dpb");
-
-    // bruce 060101 moved the rest of this function into the start of everythingElse
-    // since it depends on parameters set by the client code after this init method runs,
-    // but then had to move initializeBondTable back here to fix a bug (since mmp reading
-    // depends on it)
     initializeBondTable();
+    
     return finish_python_call(Py_None);
 }
 
@@ -380,8 +335,6 @@ everythingElse(void) // WARNING: this duplicates some code from simulator.c
     
     // wware 060109  python exception handling
     start_python_call();
-    // bruce 060101 moved this section here, from the end of initsimhelp,
-    // since it depends on parameters set by the client code after that init method runs
 
     if (TraceFileName != NULL) {
 	TraceFile = fopen(TraceFileName, "w");
@@ -418,8 +371,6 @@ everythingElse(void) // WARNING: this duplicates some code from simulator.c
     // ##e should print options set before run, but it's too early to do that in this code
 
     if (IterPerFrame <= 0) IterPerFrame = 1;
-    // initializeBondTable(); // this had to be done in initsimhelp instead [bruce 060101]
-    // end of section moved by bruce 060101
 
     constrainGlobals();
     traceHeader(part);
diff --git a/sim/src/simulator.c b/sim/src/simulator.c
index dee529b89..0df5208c4 100755
--- a/sim/src/simulator.c
+++ b/sim/src/simulator.c
@@ -95,8 +95,7 @@ usage(void)
                     specify IDKey\n\
    -K<int>, --key-record-interval=<int>\n\
                     number of delta frames between key frames\n\
-   -r, --repress-frame-numbers\n\
-                    repress the printing of frame numbers\n\
+   -r               report frame numbers\n\
    -o<string>, --output-file=<string>\n\
                     output file name (otherwise same as input)\n\
    -q<string>, --trace-file=<string>\n\
@@ -202,7 +201,6 @@ static const struct option option_vec[] = {
     { "output-format-2", no_argument, NULL, 'N' },
     { "id-key", required_argument, NULL, 'I' },
     { "key-record-interval", required_argument, NULL, 'K' },
-    { "repress-frame-numbers", no_argument, NULL, 'r' },
     { "debug", required_argument, NULL, 'D' },
     { "output-file", required_argument, NULL, 'o' },
     { "trace-file", required_argument, NULL, 'q' },
@@ -363,7 +361,7 @@ main(int argc, char **argv)
 	    KeyRecordInterval = atoi(optarg);
 	    break;
 	case 'r':
-	    PrintFrameNums = 0;
+	    PrintFrameNums = 1;
 	    break;
 	case 'D':
 	    n = atoi(optarg);
diff --git a/sim/src/tests.py b/sim/src/tests.py
index 4931d5643..d9fc0b456 100755
--- a/sim/src/tests.py
+++ b/sim/src/tests.py
@@ -927,11 +927,19 @@ class PyrexTest(TimedTest):
             pass
 
     def run(self):
-        import sim
         lac = LengthAngleComparison(self.base + ".mmp")
-        s = sim.Minimize(self.base + ".mmp")
+        import sim
+        s = sim.theSimulator()
+        s.reinitGlobals()
+        inputfile = self.base + ".mmp"
+        outputfile = self.base + ".xyz"
+        s.InputFileName = inputfile
+        s.OutputFileName = outputfile
+        s.ToMinimize = 1
+        s.DumpAsText = 1
+        s.OutputFormat = 0
         s.Temperature = 300
-        s.go()
+        s.go(frame_callback=None, trace_callback=None)
         lac.compare(self.base + ".xyz", self.base + ".xyzcmp",
                     LENGTH_TOLERANCE, ANGLE_TOLERANCE)
 
@@ -1120,7 +1128,6 @@ RANKED_BY_RUNTIME = [
     'test_reordering_jigs_or_chunks_03_thermo_rmotor_anchor_stat_reordering_4',
     'test_reordering_jigs_or_chunks_05_thermo_lmotor_anchor_measurement_jigs_reordering_3',
     'test_reordering_jigs_or_chunks_04_thermo_lmotor_anchor_stat_reordering_2',
-    'test_callWrongSimulatorObject',
     'test_motors_030_rotarymotor_and_linear_motor_attached_to_same_atoms',
     'test_floppy_organics_C4H8',
     'test_reordering_jigs_or_chunks_03_thermo_rmotor_anchor_stat_reordering_6',
@@ -1198,7 +1205,6 @@ RANKED_BY_RUNTIME = [
     'test_jigs_to_several_atoms_006_anchors_to_100_atoms',
     'test_motors_005_linearmotor_negative_force_and_positive_stiffness',
     'test_heteroatom_organics_Al_ADAM_C3v',
-    'test_dpbFileShouldBeBinaryAfterMinimize',
     'test_heteroatom_organics_ADAMframe_AlH_Cs',
     'test_minimize_0012',
     'test_jigs_to_several_atoms_004_linearmotor_to_100_atoms',
@@ -1330,15 +1336,6 @@ try:
             finally:
                 try: TimedTest.finish(self)
                 except EarlyTermination: pass
-        def test_dpbFileShouldBeBinaryAfterMinimize(self):
-            self.methodname = "test_dpbFileShouldBeBinaryAfterMinimize"
-            try: TimedTest.start(self)
-            except EarlyTermination: return
-            try:
-                sim.Tests.test_dpbFileShouldBeBinaryAfterMinimize(self)
-            finally:
-                try: TimedTest.finish(self)
-                except EarlyTermination: pass
         def test_badCallback1(self):
             self.methodname = "test_badCallback1"
             try: TimedTest.start(self)
@@ -1366,15 +1363,6 @@ try:
             finally:
                 try: TimedTest.finish(self)
                 except EarlyTermination: pass
-        def test_callWrongSimulatorObject(self):
-            self.methodname = "test_callWrongSimulatorObject"
-            try: TimedTest.start(self)
-            except EarlyTermination: return
-            try:
-                sim.Tests.test_callWrongSimulatorObject(self)
-            finally:
-                try: TimedTest.finish(self)
-                except EarlyTermination: pass
         
     baseClass = PyrexUnitTests
 except ImportError:
@@ -1716,7 +1704,14 @@ class Tests(baseClass):
         class Foo(PyrexTest):
             def run(self):
                 import sim
-                s = sim.Dynamics("tests/dynamics/test_0002.mmp")
+                s = sim.theSimulator()
+
+                s.reinitGlobals()
+                s.InputFileName = "tests/dynamics/test_0002.mmp"
+                s.OutputFileName = "tests/dynamics/test_0002.dpb"
+                s.ToMinimize = 0
+                s.DumpAsText = 0
+                s.OutputFormat = 1
                 s.NumFrames = 100
                 s.PrintFrameNums = 0
                 s.IterPerFrame = 10
author	Eric Messick <ericm@nanorex.com>	2008-01-24 05:59:06 +0000
committer	Eric Messick <ericm@nanorex.com>	2008-01-24 05:59:06 +0000
commit	4e0cd140c2144dda21cff23d81afc450c8c5d2b3 (patch)
tree	6a5ed69f98664ff8b72dbe25bb621f35c4ed37b7 /sim
parent	93027d05c213b3092c624b6ee45543c2b9e1cf89 (diff)
download	nanoengineer-4e0cd140c2144dda21cff23d81afc450c8c5d2b3.tar.gz nanoengineer-4e0cd140c2144dda21cff23d81afc450c8c5d2b3.zip