Unverified Commit 626ca25d authored by Steve Plimpton's avatar Steve Plimpton Committed by GitHub
Browse files

Merge pull request #830 from akohlmey/more-fixes-for-stable 

More small fixes for stable release
parents 8d6fbd98 63c0a35f

lib/colvars/Makefile.deps

+55 −57
Original line number Diff line number Diff line 


$(COLVARS_OBJ_DIR)colvaratoms.o: colvaratoms.cpp colvarmodule.h \

 colvars_version.h colvartypes.h colvarproxy.h colvarvalue.h \

 colvars_version.h colvarproxy.h colvarvalue.h colvartypes.h \

 colvarparse.h colvaratoms.h colvardeps.h

$(COLVARS_OBJ_DIR)colvarbias_abf.o: colvarbias_abf.cpp colvarmodule.h \

 colvars_version.h colvartypes.h colvarproxy.h colvarvalue.h colvar.h \

 colvars_version.h colvarproxy.h colvarvalue.h colvartypes.h colvar.h \

 colvarparse.h colvardeps.h lepton/include/Lepton.h \

 lepton/include/lepton/CompiledExpression.h \

 lepton/include/lepton/ExpressionTreeNode.h \
@@ -16,9 +16,9 @@ $(COLVARS_OBJ_DIR)colvarbias_abf.o: colvarbias_abf.cpp colvarmodule.h \ 
 lepton/include/lepton/ParsedExpression.h lepton/include/lepton/Parser.h \

 colvarbias_abf.h colvarbias.h colvargrid.h colvar_UIestimator.h

$(COLVARS_OBJ_DIR)colvarbias_alb.o: colvarbias_alb.cpp colvarmodule.h \

 colvars_version.h colvartypes.h colvarproxy.h colvarvalue.h \

 colvarbias_alb.h colvar.h colvarparse.h colvardeps.h \

 lepton/include/Lepton.h lepton/include/lepton/CompiledExpression.h \

 colvars_version.h colvarbias.h colvar.h colvarvalue.h colvartypes.h \

 colvarparse.h colvardeps.h lepton/include/Lepton.h \

 lepton/include/lepton/CompiledExpression.h \

 lepton/include/lepton/ExpressionTreeNode.h \

 lepton/include/lepton/windowsIncludes.h \

 lepton/include/lepton/CustomFunction.h \
@@ -27,9 +27,9 @@ $(COLVARS_OBJ_DIR)colvarbias_alb.o: colvarbias_alb.cpp colvarmodule.h \ 
 lepton/include/lepton/Operation.h lepton/include/lepton/CustomFunction.h \

 lepton/include/lepton/Exception.h \

 lepton/include/lepton/ParsedExpression.h lepton/include/lepton/Parser.h \

 colvarbias.h

 colvarbias_alb.h

$(COLVARS_OBJ_DIR)colvarbias.o: colvarbias.cpp colvarmodule.h \

 colvars_version.h colvartypes.h colvarproxy.h colvarvalue.h colvarbias.h \

 colvars_version.h colvarproxy.h colvarvalue.h colvartypes.h colvarbias.h \

 colvar.h colvarparse.h colvardeps.h lepton/include/Lepton.h \

 lepton/include/lepton/CompiledExpression.h \

 lepton/include/lepton/ExpressionTreeNode.h \
@@ -42,8 +42,8 @@ $(COLVARS_OBJ_DIR)colvarbias.o: colvarbias.cpp colvarmodule.h \ 
 lepton/include/lepton/ParsedExpression.h lepton/include/lepton/Parser.h \

 colvargrid.h

$(COLVARS_OBJ_DIR)colvarbias_histogram.o: colvarbias_histogram.cpp \

 colvarmodule.h colvars_version.h colvartypes.h colvarproxy.h \

 colvarvalue.h colvar.h colvarparse.h colvardeps.h \

 colvarmodule.h colvars_version.h colvarproxy.h colvarvalue.h \

 colvartypes.h colvar.h colvarparse.h colvardeps.h \

 lepton/include/Lepton.h lepton/include/lepton/CompiledExpression.h \

 lepton/include/lepton/ExpressionTreeNode.h \

 lepton/include/lepton/windowsIncludes.h \
@@ -54,9 +54,9 @@ $(COLVARS_OBJ_DIR)colvarbias_histogram.o: colvarbias_histogram.cpp \ 
 lepton/include/lepton/Exception.h \

 lepton/include/lepton/ParsedExpression.h lepton/include/lepton/Parser.h \

 colvarbias_histogram.h colvarbias.h colvargrid.h

$(COLVARS_OBJ_DIR)colvarbias_meta.o: colvarbias_meta.cpp colvar.h \

 colvarmodule.h colvars_version.h colvartypes.h colvarproxy.h \

 colvarvalue.h colvarparse.h colvardeps.h lepton/include/Lepton.h \

$(COLVARS_OBJ_DIR)colvarbias_meta.o: colvarbias_meta.cpp colvarmodule.h \

 colvars_version.h colvarproxy.h colvarvalue.h colvartypes.h colvar.h \

 colvarparse.h colvardeps.h lepton/include/Lepton.h \

 lepton/include/lepton/CompiledExpression.h \

 lepton/include/lepton/ExpressionTreeNode.h \

 lepton/include/lepton/windowsIncludes.h \
@@ -68,8 +68,8 @@ $(COLVARS_OBJ_DIR)colvarbias_meta.o: colvarbias_meta.cpp colvar.h \ 
 lepton/include/lepton/ParsedExpression.h lepton/include/lepton/Parser.h \

 colvarbias_meta.h colvarbias.h colvargrid.h

$(COLVARS_OBJ_DIR)colvarbias_restraint.o: colvarbias_restraint.cpp \

 colvarmodule.h colvars_version.h colvartypes.h colvarproxy.h \

 colvarvalue.h colvarbias_restraint.h colvarbias.h colvar.h colvarparse.h \

 colvarmodule.h colvars_version.h colvarproxy.h colvarvalue.h \

 colvartypes.h colvarbias_restraint.h colvarbias.h colvar.h colvarparse.h \

 colvardeps.h lepton/include/Lepton.h \

 lepton/include/lepton/CompiledExpression.h \

 lepton/include/lepton/ExpressionTreeNode.h \
@@ -81,9 +81,9 @@ $(COLVARS_OBJ_DIR)colvarbias_restraint.o: colvarbias_restraint.cpp \ 
 lepton/include/lepton/Exception.h \

 lepton/include/lepton/ParsedExpression.h lepton/include/lepton/Parser.h

$(COLVARS_OBJ_DIR)colvarcomp_angles.o: colvarcomp_angles.cpp \

 colvarmodule.h colvars_version.h colvartypes.h colvarproxy.h \

 colvarvalue.h colvar.h colvarparse.h colvardeps.h \

 lepton/include/Lepton.h lepton/include/lepton/CompiledExpression.h \

 colvarmodule.h colvars_version.h colvar.h colvarvalue.h colvartypes.h \

 colvarparse.h colvardeps.h lepton/include/Lepton.h \

 lepton/include/lepton/CompiledExpression.h \

 lepton/include/lepton/ExpressionTreeNode.h \

 lepton/include/lepton/windowsIncludes.h \

 lepton/include/lepton/CustomFunction.h \
@@ -92,10 +92,10 @@ $(COLVARS_OBJ_DIR)colvarcomp_angles.o: colvarcomp_angles.cpp \ 
 lepton/include/lepton/Operation.h lepton/include/lepton/CustomFunction.h \

 lepton/include/lepton/Exception.h \

 lepton/include/lepton/ParsedExpression.h lepton/include/lepton/Parser.h \

 colvarcomp.h colvaratoms.h

 colvarcomp.h colvaratoms.h colvarproxy.h

$(COLVARS_OBJ_DIR)colvarcomp_coordnums.o: colvarcomp_coordnums.cpp \

 colvarmodule.h colvars_version.h colvartypes.h colvarproxy.h \

 colvarvalue.h colvarparse.h colvaratoms.h colvardeps.h colvar.h \

 colvarmodule.h colvars_version.h colvarparse.h colvarvalue.h \

 colvartypes.h colvaratoms.h colvarproxy.h colvardeps.h colvar.h \

 lepton/include/Lepton.h lepton/include/lepton/CompiledExpression.h \

 lepton/include/lepton/ExpressionTreeNode.h \

 lepton/include/lepton/windowsIncludes.h \
@@ -107,8 +107,8 @@ $(COLVARS_OBJ_DIR)colvarcomp_coordnums.o: colvarcomp_coordnums.cpp \ 
 lepton/include/lepton/ParsedExpression.h lepton/include/lepton/Parser.h \

 colvarcomp.h

$(COLVARS_OBJ_DIR)colvarcomp.o: colvarcomp.cpp colvarmodule.h \

 colvars_version.h colvartypes.h colvarproxy.h colvarvalue.h colvar.h \

 colvarparse.h colvardeps.h lepton/include/Lepton.h \

 colvars_version.h colvarvalue.h colvartypes.h colvar.h colvarparse.h \

 colvardeps.h lepton/include/Lepton.h \

 lepton/include/lepton/CompiledExpression.h \

 lepton/include/lepton/ExpressionTreeNode.h \

 lepton/include/lepton/windowsIncludes.h \
@@ -118,11 +118,11 @@ $(COLVARS_OBJ_DIR)colvarcomp.o: colvarcomp.cpp colvarmodule.h \ 
 lepton/include/lepton/Operation.h lepton/include/lepton/CustomFunction.h \

 lepton/include/lepton/Exception.h \

 lepton/include/lepton/ParsedExpression.h lepton/include/lepton/Parser.h \

 colvarcomp.h colvaratoms.h

 colvarcomp.h colvaratoms.h colvarproxy.h

$(COLVARS_OBJ_DIR)colvarcomp_distances.o: colvarcomp_distances.cpp \

 colvarmodule.h colvars_version.h colvartypes.h colvarproxy.h \

 colvarvalue.h colvarparse.h colvar.h colvardeps.h \

 lepton/include/Lepton.h lepton/include/lepton/CompiledExpression.h \

 colvarmodule.h colvars_version.h colvarvalue.h colvartypes.h \

 colvarparse.h colvar.h colvardeps.h lepton/include/Lepton.h \

 lepton/include/lepton/CompiledExpression.h \

 lepton/include/lepton/ExpressionTreeNode.h \

 lepton/include/lepton/windowsIncludes.h \

 lepton/include/lepton/CustomFunction.h \
@@ -131,11 +131,11 @@ $(COLVARS_OBJ_DIR)colvarcomp_distances.o: colvarcomp_distances.cpp \ 
 lepton/include/lepton/Operation.h lepton/include/lepton/CustomFunction.h \

 lepton/include/lepton/Exception.h \

 lepton/include/lepton/ParsedExpression.h lepton/include/lepton/Parser.h \

 colvarcomp.h colvaratoms.h

 colvarcomp.h colvaratoms.h colvarproxy.h

$(COLVARS_OBJ_DIR)colvarcomp_protein.o: colvarcomp_protein.cpp \

 colvarmodule.h colvars_version.h colvartypes.h colvarproxy.h \

 colvarvalue.h colvarparse.h colvar.h colvardeps.h \

 lepton/include/Lepton.h lepton/include/lepton/CompiledExpression.h \

 colvarmodule.h colvars_version.h colvarvalue.h colvartypes.h \

 colvarparse.h colvar.h colvardeps.h lepton/include/Lepton.h \

 lepton/include/lepton/CompiledExpression.h \

 lepton/include/lepton/ExpressionTreeNode.h \

 lepton/include/lepton/windowsIncludes.h \

 lepton/include/lepton/CustomFunction.h \
@@ -144,11 +144,11 @@ $(COLVARS_OBJ_DIR)colvarcomp_protein.o: colvarcomp_protein.cpp \ 
 lepton/include/lepton/Operation.h lepton/include/lepton/CustomFunction.h \

 lepton/include/lepton/Exception.h \

 lepton/include/lepton/ParsedExpression.h lepton/include/lepton/Parser.h \

 colvarcomp.h colvaratoms.h

 colvarcomp.h colvaratoms.h colvarproxy.h

$(COLVARS_OBJ_DIR)colvarcomp_rotations.o: colvarcomp_rotations.cpp \

 colvarmodule.h colvars_version.h colvartypes.h colvarproxy.h \

 colvarvalue.h colvarparse.h colvar.h colvardeps.h \

 lepton/include/Lepton.h lepton/include/lepton/CompiledExpression.h \

 colvarmodule.h colvars_version.h colvarvalue.h colvartypes.h \

 colvarparse.h colvar.h colvardeps.h lepton/include/Lepton.h \

 lepton/include/lepton/CompiledExpression.h \

 lepton/include/lepton/ExpressionTreeNode.h \

 lepton/include/lepton/windowsIncludes.h \

 lepton/include/lepton/CustomFunction.h \
@@ -157,11 +157,10 @@ $(COLVARS_OBJ_DIR)colvarcomp_rotations.o: colvarcomp_rotations.cpp \ 
 lepton/include/lepton/Operation.h lepton/include/lepton/CustomFunction.h \

 lepton/include/lepton/Exception.h \

 lepton/include/lepton/ParsedExpression.h lepton/include/lepton/Parser.h \

 colvarcomp.h colvaratoms.h

 colvarcomp.h colvaratoms.h colvarproxy.h

$(COLVARS_OBJ_DIR)colvar.o: colvar.cpp colvarmodule.h colvars_version.h \

 colvartypes.h colvarproxy.h colvarvalue.h colvarparse.h colvar.h \

 colvardeps.h lepton/include/Lepton.h \

 lepton/include/lepton/CompiledExpression.h \

 colvarvalue.h colvartypes.h colvarparse.h colvar.h colvardeps.h \

 lepton/include/Lepton.h lepton/include/lepton/CompiledExpression.h \

 lepton/include/lepton/ExpressionTreeNode.h \

 lepton/include/lepton/windowsIncludes.h \

 lepton/include/lepton/CustomFunction.h \
@@ -170,13 +169,13 @@ $(COLVARS_OBJ_DIR)colvar.o: colvar.cpp colvarmodule.h colvars_version.h \ 
 lepton/include/lepton/Operation.h lepton/include/lepton/CustomFunction.h \

 lepton/include/lepton/Exception.h \

 lepton/include/lepton/ParsedExpression.h lepton/include/lepton/Parser.h \

 colvarcomp.h colvaratoms.h colvarscript.h colvarbias.h

$(COLVARS_OBJ_DIR)colvardeps.o: colvardeps.cpp colvardeps.h \

 colvarmodule.h colvars_version.h colvartypes.h colvarproxy.h \

 colvarvalue.h colvarparse.h

 colvarcomp.h colvaratoms.h colvarproxy.h colvarscript.h colvarbias.h

$(COLVARS_OBJ_DIR)colvardeps.o: colvardeps.cpp colvarmodule.h \

 colvars_version.h colvarproxy.h colvarvalue.h colvartypes.h colvardeps.h \

 colvarparse.h

$(COLVARS_OBJ_DIR)colvargrid.o: colvargrid.cpp colvarmodule.h \

 colvars_version.h colvartypes.h colvarproxy.h colvarvalue.h \

 colvarparse.h colvar.h colvardeps.h lepton/include/Lepton.h \

 colvars_version.h colvarvalue.h colvartypes.h colvarparse.h colvar.h \

 colvardeps.h lepton/include/Lepton.h \

 lepton/include/lepton/CompiledExpression.h \

 lepton/include/lepton/ExpressionTreeNode.h \

 lepton/include/lepton/windowsIncludes.h \
@@ -186,10 +185,10 @@ $(COLVARS_OBJ_DIR)colvargrid.o: colvargrid.cpp colvarmodule.h \ 
 lepton/include/lepton/Operation.h lepton/include/lepton/CustomFunction.h \

 lepton/include/lepton/Exception.h \

 lepton/include/lepton/ParsedExpression.h lepton/include/lepton/Parser.h \

 colvarcomp.h colvaratoms.h colvargrid.h

 colvarcomp.h colvaratoms.h colvarproxy.h colvargrid.h

$(COLVARS_OBJ_DIR)colvarmodule.o: colvarmodule.cpp colvarmodule.h \

 colvars_version.h colvartypes.h colvarproxy.h colvarvalue.h \

 colvarparse.h colvar.h colvardeps.h lepton/include/Lepton.h \

 colvars_version.h colvarparse.h colvarvalue.h colvartypes.h \

 colvarproxy.h colvar.h colvardeps.h lepton/include/Lepton.h \

 lepton/include/lepton/CompiledExpression.h \

 lepton/include/lepton/ExpressionTreeNode.h \

 lepton/include/lepton/windowsIncludes.h \
@@ -203,10 +202,9 @@ $(COLVARS_OBJ_DIR)colvarmodule.o: colvarmodule.cpp colvarmodule.h \ 
 colvarbias_alb.h colvarbias_histogram.h colvarbias_meta.h \

 colvarbias_restraint.h colvarscript.h colvaratoms.h colvarcomp.h

$(COLVARS_OBJ_DIR)colvarparse.o: colvarparse.cpp colvarmodule.h \

 colvars_version.h colvartypes.h colvarproxy.h colvarvalue.h \

 colvarparse.h

 colvars_version.h colvarvalue.h colvartypes.h colvarparse.h

$(COLVARS_OBJ_DIR)colvarproxy.o: colvarproxy.cpp colvarmodule.h \

 colvars_version.h colvartypes.h colvarproxy.h colvarvalue.h \

 colvars_version.h colvarproxy.h colvarvalue.h colvartypes.h \

 colvarscript.h colvarbias.h colvar.h colvarparse.h colvardeps.h \

 lepton/include/Lepton.h lepton/include/lepton/CompiledExpression.h \

 lepton/include/lepton/ExpressionTreeNode.h \
@@ -219,9 +217,9 @@ $(COLVARS_OBJ_DIR)colvarproxy.o: colvarproxy.cpp colvarmodule.h \ 
 lepton/include/lepton/ParsedExpression.h lepton/include/lepton/Parser.h \

 colvaratoms.h

$(COLVARS_OBJ_DIR)colvarscript.o: colvarscript.cpp colvarscript.h \

 colvarmodule.h colvars_version.h colvartypes.h colvarproxy.h \

 colvarvalue.h colvarbias.h colvar.h colvarparse.h colvardeps.h \

 lepton/include/Lepton.h lepton/include/lepton/CompiledExpression.h \

 colvarmodule.h colvars_version.h colvarvalue.h colvartypes.h \

 colvarbias.h colvar.h colvarparse.h colvardeps.h lepton/include/Lepton.h \

 lepton/include/lepton/CompiledExpression.h \

 lepton/include/lepton/ExpressionTreeNode.h \

 lepton/include/lepton/windowsIncludes.h \

 lepton/include/lepton/CustomFunction.h \
@@ -229,9 +227,9 @@ $(COLVARS_OBJ_DIR)colvarscript.o: colvarscript.cpp colvarscript.h \ 
 lepton/include/lepton/ExpressionTreeNode.h \

 lepton/include/lepton/Operation.h lepton/include/lepton/CustomFunction.h \

 lepton/include/lepton/Exception.h \

 lepton/include/lepton/ParsedExpression.h lepton/include/lepton/Parser.h

 lepton/include/lepton/ParsedExpression.h lepton/include/lepton/Parser.h \

 colvarproxy.h

$(COLVARS_OBJ_DIR)colvartypes.o: colvartypes.cpp colvarmodule.h \

 colvars_version.h colvartypes.h colvarproxy.h colvarvalue.h \

 colvarparse.h

 colvars_version.h colvartypes.h colvarparse.h colvarvalue.h

$(COLVARS_OBJ_DIR)colvarvalue.o: colvarvalue.cpp colvarmodule.h \

 colvars_version.h colvartypes.h colvarproxy.h colvarvalue.h
 
 colvars_version.h colvarvalue.h colvartypes.h

lib/reax/reax_charges.F

+1 −1
Original line number Diff line number Diff line
@@ -78,7 +78,7 @@ c$$$ end if 
      SWC3= 140.0D0*(SWA3*SWB+3.0D0*SWA2*SWB2+SWA*SWB3)/D7

      SWC2=-210.0D0*(SWA3*SWB2+SWA2*SWB3)/D7

      SWC1= 140.0D0*SWA3*SWB3/D7

      SWC0=(-35.0D0*SWA3*SWB2*SWB2+21.0D0*SWA2*SWB3*SWB2+

      SWC0=(-35.0D0*SWA3*SWB2*SWB2+21.0D0*SWA2*SWB3*SWB2-

     $7.0D0*SWA*SWB3*SWB3+SWB3*SWB3*SWB)/D7

 

      return

src/KOKKOS/pair_reaxc_kokkos.cpp

+1 −1
Original line number Diff line number Diff line
@@ -358,7 +358,7 @@ void PairReaxCKokkos<DeviceType>::init_md() 
  k_tap.h_view(3) = 140.0 * (swa3*swb + 3.0*swa2*swb2 + swa*swb3 ) / d7;

  k_tap.h_view(2) =-210.0 * (swa3*swb2 + swa2*swb3) / d7;

  k_tap.h_view(1) = 140.0 * swa3 * swb3 / d7;

  k_tap.h_view(0) = (-35.0*swa3*swb2*swb2 + 21.0*swa2*swb3*swb2 +

  k_tap.h_view(0) = (-35.0*swa3*swb2*swb2 + 21.0*swa2*swb3*swb2 -

                     7.0*swa*swb3*swb3 + swb3*swb3*swb ) / d7;



  k_tap.template modify<LMPHostType>();

src/QEQ/fix_qeq_shielded.cpp

+1 −1
Original line number Diff line number Diff line
@@ -105,7 +105,7 @@ void FixQEqShielded::init_shielding() 
  Tap[3] = 140.0 * (swa3*swb + 3.0*swa2*swb2 + swa*swb3 ) / d7;

  Tap[2] =-210.0 * (swa3*swb2 + swa2*swb3) / d7;

  Tap[1] = 140.0 * swa3 * swb3 / d7;

  Tap[0] = (-35.0*swa3*swb2*swb2 + 21.0*swa2*swb3*swb2 +

  Tap[0] = (-35.0*swa3*swb2*swb2 + 21.0*swa2*swb3*swb2 -

            7.0*swa*swb3*swb3 + swb3*swb3*swb ) / d7;

}

src/REAX/pair_reax.cpp

+2 −7
Original line number Diff line number Diff line
@@ -172,10 +172,6 @@ void PairREAX::compute(int eflag, int vflag) 


  FORTRAN(srtbon1, SRTBON1)(&iprune, &ihb, &hbcut, &ihbnew, &itripstaball);



  // communicate with other processors for the atomic bond order calculations



  FORTRAN(cbkabo, CBKABO).abo;



  // communicate local atomic bond order to ghost atomic bond order



  packflag = 0;
@@ -720,7 +716,7 @@ void PairREAX::taper_setup() 
  swc3= 140.0e0*(swa3*swb+3.0e0*swa2*swb2+swa*swb3)/d7;

  swc2=-210.0e0*(swa3*swb2+swa2*swb3)/d7;

  swc1= 140.0e0*swa3*swb3/d7;

  swc0=(-35.0e0*swa3*swb2*swb2+21.0e0*swa2*swb3*swb2+

  swc0=(-35.0e0*swa3*swb2*swb2+21.0e0*swa2*swb3*swb2-

        7.0e0*swa*swb3*swb3+swb3*swb3*swb)/d7;

}
@@ -943,7 +939,7 @@ void PairREAX::cg_solve(const int & nlocal, const int & nghost, 
                        double aval[], int acol_ind[], int arow_ptr[],

                        double x[], double b[])

{

  double one, zero, rho, rho_old, alpha, beta, gamma;

  double one, rho, rho_old, alpha, beta, gamma;

  int iter, maxiter;

  int n;

  double sumtmp;
@@ -963,7 +959,6 @@ void PairREAX::cg_solve(const int & nlocal, const int & nghost, 
  n = nlocal+nghost+1;



  one = 1.0;

  zero = 0.0;

  maxiter = 100;



  for (int i = 0; i < n; i++) w[i] = 0;

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