From 31260711d6dbce946c9b975c6582b422fdc216e1 Mon Sep 17 00:00:00 2001 From: "Daniel R. Roe" Date: Thu, 9 Jan 2020 10:48:57 -0500 Subject: [PATCH 1/6] DRR - Add TIP4P gist test --- test/Test_GIST_Order/RunTest.sh | 18 ++- test/Test_GIST_Order/tip4p.dat.save | 3 + test/Test_GIST_Order/tip4pew.cluster.parm7 | 163 +++++++++++++++++++++ test/Test_GIST_Order/tip4pew.cluster.rst7 | 13 ++ 4 files changed, 193 insertions(+), 4 deletions(-) create mode 100644 test/Test_GIST_Order/tip4p.dat.save create mode 100644 test/Test_GIST_Order/tip4pew.cluster.parm7 create mode 100644 test/Test_GIST_Order/tip4pew.cluster.rst7 diff --git a/test/Test_GIST_Order/RunTest.sh b/test/Test_GIST_Order/RunTest.sh index 58a7341acd..4039b01055 100755 --- a/test/Test_GIST_Order/RunTest.sh +++ b/test/Test_GIST_Order/RunTest.sh @@ -2,22 +2,32 @@ . ../MasterTest.sh -CleanFiles gist.in gist-*.dx gistout.dat +CleanFiles gist.in gist-*.dx gistout.dat tip4p.dat -TESTNAME='GIST tetrahedral water cluster test' +TESTNAME='GIST tetrahedral water cluster tests' Requires notparallel INPUT="-i gist.in" +UNITNAME='TIP3P water cluster' cat > gist.in < gist.in < Date: Thu, 9 Jan 2020 10:51:16 -0500 Subject: [PATCH 2/6] DRR - Add GIST TIP5P test --- test/Test_GIST_Order/RunTest.sh | 17 ++- test/Test_GIST_Order/tip5p.cluster.parm7 | 178 +++++++++++++++++++++++ test/Test_GIST_Order/tip5p.cluster.rst7 | 16 ++ test/Test_GIST_Order/tip5p.dat.save | 3 + 4 files changed, 211 insertions(+), 3 deletions(-) create mode 100644 test/Test_GIST_Order/tip5p.cluster.parm7 create mode 100644 test/Test_GIST_Order/tip5p.cluster.rst7 create mode 100644 test/Test_GIST_Order/tip5p.dat.save diff --git a/test/Test_GIST_Order/RunTest.sh b/test/Test_GIST_Order/RunTest.sh index 4039b01055..6cfe0ab4b9 100755 --- a/test/Test_GIST_Order/RunTest.sh +++ b/test/Test_GIST_Order/RunTest.sh @@ -2,14 +2,14 @@ . ../MasterTest.sh -CleanFiles gist.in gist-*.dx gistout.dat tip4p.dat +CleanFiles gist.in gist-*.dx gistout.dat tip4p.dat tip5p.dat TESTNAME='GIST tetrahedral water cluster tests' Requires notparallel INPUT="-i gist.in" -UNITNAME='TIP3P water cluster' +UNITNAME='TIP3P water cluster test' cat > gist.in < gist.in < gist.in < Date: Thu, 9 Jan 2020 10:53:49 -0500 Subject: [PATCH 3/6] DRR - Remove extra whitespace from trajectory - not sure how that got in there... --- test/Test_GIST_Order/test_gist-center.crd | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/test/Test_GIST_Order/test_gist-center.crd b/test/Test_GIST_Order/test_gist-center.crd index 67a9558019..82850430ff 100644 --- a/test/Test_GIST_Order/test_gist-center.crd +++ b/test/Test_GIST_Order/test_gist-center.crd @@ -4,4 +4,4 @@ Cpptraj Generated trajectory 0.000 -0.254 0.021 -0.923 0.849 0.441 0.025 -2.691 0.685 0.703 -2.666 0.593 1.656 -1.834 0.375 0.411 2.133 1.334 0.972 1.864 1.133 1.868 2.207 2.288 0.952 - 32.472 32.489 32.464 + 32.472 32.489 32.464 From 64b19644a8826d893f3b18d1c939e2b83d23f1c7 Mon Sep 17 00:00:00 2001 From: "Daniel R. Roe" Date: Thu, 9 Jan 2020 11:27:26 -0500 Subject: [PATCH 4/6] DRR - Fix order calculation for water models with extra points --- src/Action_GIST.cpp | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/Action_GIST.cpp b/src/Action_GIST.cpp index 196e8574f2..6ebaeb4370 100644 --- a/src/Action_GIST.cpp +++ b/src/Action_GIST.cpp @@ -663,7 +663,7 @@ void Action_GIST::NonbondEnergy(Frame const& frameIn, Topology const& topIn) // Action_GIST::Order() void Action_GIST::Order(Frame const& frameIn) { // Loop over all solvent molecules that are on the grid - for (unsigned int gidx = 0; gidx < N_ON_GRID_; gidx += 3) + for (unsigned int gidx = 0; gidx < N_ON_GRID_; gidx += nMolAtoms_) { int oidx1 = OnGrid_idxs_[gidx]; int voxel1 = atom_voxel_[oidx1]; From a48ae25219389c1a5810e19320dde4b125f70fa8 Mon Sep 17 00:00:00 2001 From: "Daniel R. Roe" Date: Thu, 9 Jan 2020 11:28:41 -0500 Subject: [PATCH 5/6] DRR - Update order output; values should all match --- test/Test_GIST_Order/tip4p.dat.save | 2 +- test/Test_GIST_Order/tip5p.dat.save | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/test/Test_GIST_Order/tip4p.dat.save b/test/Test_GIST_Order/tip4p.dat.save index db04497813..3e70ce0904 100644 --- a/test/Test_GIST_Order/tip4p.dat.save +++ b/test/Test_GIST_Order/tip4p.dat.save @@ -1,3 +1,3 @@ GIST Output, information printed per voxel voxel xcoord ycoord zcoord population g_O g_H dTStrans-dens(kcal/mol/A^3) dTStrans-norm(kcal/mol) dTSorient-dens(kcal/mol/A^3) dTSorient-norm(kcal/mol) dTSsix-dens(kcal/mol/A^3) dTSsix-norm (kcal/mol) Esw-dens(kcal/mol/A^3) Esw-norm(kcal/mol) Eww-dens(kcal/mol/A^3) Eww-norm-unref(kcal/mol) Dipole_x-dens(D/A^3) Dipole_y-dens(D/A^3) Dipole_z-dens(D/A^3) Dipole-dens(D/A^3) neighbor-dens(1/A^3) neighbor-norm order-norm -0 0.5 0.5 0.5 1 30.03 15.015 0 0 0 0 0 0 0 0 0 0 1.17821 0.914938 -1.77876 2.32148 4 4 1.56786 +0 0.5 0.5 0.5 1 30.03 15.015 0 0 0 0 0 0 0 0 0 0 1.17821 0.914938 -1.77876 2.32148 4 4 0.958873 diff --git a/test/Test_GIST_Order/tip5p.dat.save b/test/Test_GIST_Order/tip5p.dat.save index 39cb8c684d..c843f8ad3e 100644 --- a/test/Test_GIST_Order/tip5p.dat.save +++ b/test/Test_GIST_Order/tip5p.dat.save @@ -1,3 +1,3 @@ GIST Output, information printed per voxel voxel xcoord ycoord zcoord population g_O g_H dTStrans-dens(kcal/mol/A^3) dTStrans-norm(kcal/mol) dTSorient-dens(kcal/mol/A^3) dTSorient-norm(kcal/mol) dTSsix-dens(kcal/mol/A^3) dTSsix-norm (kcal/mol) Esw-dens(kcal/mol/A^3) Esw-norm(kcal/mol) Eww-dens(kcal/mol/A^3) Eww-norm-unref(kcal/mol) Dipole_x-dens(D/A^3) Dipole_y-dens(D/A^3) Dipole_z-dens(D/A^3) Dipole-dens(D/A^3) neighbor-dens(1/A^3) neighbor-norm order-norm -0 0.5 0.5 0.5 1 30.03 15.015 0 0 0 0 0 0 0 0 0 0 0.545385 0.54656 -1.55994 1.74057 4 4 1.44657 +0 0.5 0.5 0.5 1 30.03 15.015 0 0 0 0 0 0 0 0 0 0 0.545385 0.54656 -1.55994 1.74057 4 4 0.958873 From 19e4686af7678fc27ab88be4765c1e280bc544f5 Mon Sep 17 00:00:00 2001 From: "Daniel R. Roe" Date: Thu, 9 Jan 2020 11:35:17 -0500 Subject: [PATCH 6/6] DRR - Use forward declares. --- src/Action_GIST.cpp | 1 + src/Action_GIST.h | 4 ++-- 2 files changed, 3 insertions(+), 2 deletions(-) diff --git a/src/Action_GIST.cpp b/src/Action_GIST.cpp index 6ebaeb4370..c928fa26e3 100644 --- a/src/Action_GIST.cpp +++ b/src/Action_GIST.cpp @@ -3,6 +3,7 @@ #include "Action_GIST.h" #include "CpptrajStdio.h" #include "Constants.h" +#include "DataSet_MatrixFlt.h" #include "DataSet_GridFlt.h" #include "DataSet_GridDbl.h" #include "ProgressBar.h" diff --git a/src/Action_GIST.h b/src/Action_GIST.h index c6d0b0f217..575850dc59 100644 --- a/src/Action_GIST.h +++ b/src/Action_GIST.h @@ -2,9 +2,9 @@ #define INC_ACTION_GIST_H #include "Action.h" #include "ImagedAction.h" -#include "DataSet_3D.h" -#include "DataSet_MatrixFlt.h" #include "Timer.h" +class DataSet_3D; +class DataSet_MatrixFlt; /// Class for applying Grid Inhomogenous Solvation Theory /** \author Daniel R. Roe */