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drroeDaniel R. Roe
drroe
and
Daniel R. Roe
authored
Fix a potential segfault when using COORDS data sets (#900)
* Do not try to set force and velocity if not allocated in the output frame. * Add 2drms test on coords with velocity info. Will be all zero but would catch the previously fixed segfault * Revision bump for COORDS potential segfault fix Co-authored-by: Daniel R. Roe <[email protected]>
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4 files changed

+102
-6
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4 files changed

+102
-6
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‎src/DataSet_Coords_CRD.cpp‎

Lines changed: 4 additions & 4 deletions
Original file line numberDiff line numberDiff line change
@@ -133,16 +133,16 @@ static inline void ArrayToFrame(int idx, Frame& fOut, CompactFrameArray const& f
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/** Get a frame from specified position in array. */
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void DataSet_Coords_CRD::GetFrame(int idx, Frame& fOut) {
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if (frames_.HasComponent(CoordinateInfo::POSITION)) frames_.GetToDblPtr(fOut.xAddress(), idx, CoordinateInfo::POSITION);
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if (frames_.HasComponent(CoordinateInfo::VELOCITY)) frames_.GetToDblPtr(fOut.vAddress(), idx, CoordinateInfo::VELOCITY);
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if (frames_.HasComponent(CoordinateInfo::FORCE)) frames_.GetToDblPtr(fOut.fAddress(), idx, CoordinateInfo::FORCE);
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if (frames_.HasComponent(CoordinateInfo::VELOCITY) && fOut.HasVelocity()) frames_.GetToDblPtr(fOut.vAddress(), idx, CoordinateInfo::VELOCITY);
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if (frames_.HasComponent(CoordinateInfo::FORCE) && fOut.HasForce()) frames_.GetToDblPtr(fOut.fAddress(), idx, CoordinateInfo::FORCE);
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ArrayToFrame(idx, fOut, frames_);
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}
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/** Get selected atoms from a frame from specified position in array. */
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void DataSet_Coords_CRD::GetFrame(int idx, Frame& fOut, AtomMask const& mask) {
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if (frames_.HasComponent(CoordinateInfo::POSITION)) frames_.GetToMaskDblPtr(fOut.xAddress(), mask.Selected(), idx, CoordinateInfo::POSITION);
144-
if (frames_.HasComponent(CoordinateInfo::VELOCITY)) frames_.GetToMaskDblPtr(fOut.vAddress(), mask.Selected(), idx, CoordinateInfo::VELOCITY);
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if (frames_.HasComponent(CoordinateInfo::FORCE)) frames_.GetToMaskDblPtr(fOut.fAddress(), mask.Selected(), idx, CoordinateInfo::FORCE);
144+
if (frames_.HasComponent(CoordinateInfo::VELOCITY) && fOut.HasVelocity()) frames_.GetToMaskDblPtr(fOut.vAddress(), mask.Selected(), idx, CoordinateInfo::VELOCITY);
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if (frames_.HasComponent(CoordinateInfo::FORCE) && fOut.HasForce()) frames_.GetToMaskDblPtr(fOut.fAddress(), mask.Selected(), idx, CoordinateInfo::FORCE);
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ArrayToFrame(idx, fOut, frames_);
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}
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‎src/Version.h‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -12,7 +12,7 @@
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* Whenever a number that precedes <revision> is incremented, all subsequent
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* numbers should be reset to 0.
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*/
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#define CPPTRAJ_INTERNAL_VERSION "V5.3.1"
15+
#define CPPTRAJ_INTERNAL_VERSION "V5.3.2"
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/// PYTRAJ relies on this
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#define CPPTRAJ_VERSION_STRING CPPTRAJ_INTERNAL_VERSION
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#endif

‎test/Test_2DRMS/RunTest.sh‎

Lines changed: 15 additions & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -3,7 +3,8 @@
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. ../MasterTest.sh
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# Clean
6-
CleanFiles rms.in rmsd1.dat rmsd2.dat ref.nc rmsd.mass.dat dme.dat trp.dat nofit.dat
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CleanFiles rms.in rmsd1.dat rmsd2.dat ref.nc rmsd.mass.dat dme.dat trp.dat \
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nofit.dat rgacc.dat
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TESTNAME='2D RMSD tests'
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Requires netcdf maxthreads 10
@@ -73,6 +74,19 @@ EOF
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RunCpptraj "2D RMSD test, no fitting."
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DoTest nofit.dat.save nofit.dat
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# Test 7 - coords with velocities
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TOP=''
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CRD=''
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cat > rms.in <<EOF
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parm ../rGACC.full.parm7
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for i=1;i<10;i++
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trajin ../rGACC.full.nc
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done
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2drms crd1 :1-4&!@H= out rgacc.dat nosquare2d
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EOF
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RunCpptraj "2D RMSD test, read coords with velocity info"
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DoTest rgacc.dat.save rgacc.dat
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EndTest
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exit 0

‎test/Test_2DRMS/rgacc.dat.save‎

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@@ -0,0 +1,82 @@
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# crd1
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1.000 1.000 0.000
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2.000 1.000 0.000
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3.000 1.000 0.000
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4.000 1.000 0.000
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5.000 1.000 0.000
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1.000 2.000 0.000
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1.000 4.000 0.000
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