Commit b241294e authored by Anne Gunn's avatar Anne Gunn
Browse files

Corrected two issues in code identified by valgrind: 

1) memory leaks (the subject of the original #1109) and
2) an invalid memory access (reading from beyond the end of an array).

Also:
- replaced several dynamically-allocated (calloc and free) local arrays with std::vector.
- reorganized include statements per new conventions, and
- updated messages to use strings and fmt.

Added folders and files used in manual testing and verification to examples folder.

No changes in analysis results are expected or intended. This is pure refactoring except for a bit of error message cleanup.
parent 3be06474

examples/USER/bocs/tests/README

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This folder contains a variety of input/output files for the

USER-BOCS code that exercises both error handling and all three

analysis modes (analytic, linear spline, and cubic spline).



In the absence of automated testing, the bash script, runTests.sh

may be used to generate a folder of log files which can be

compared to the baseline file set in logsCompareFileSet to

look for material changes.

examples/USER/bocs/tests/cgheptaneFileSet/cgheptane.badAnalyticCoefficients.lmp

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## Parameters initialization



units 		real

atom_style 	full



pair_style	table linear 1000

bond_style      table linear 1000

angle_style     table linear 1000

dihedral_style  none

improper_style  none

kspace_style    none



boundary 	p p p

dimension 	3

newton 		on



read_data	data.cgheptane



pair_coeff 1 1 lammps_CT_CT.table LJLJ 12.0

pair_coeff 1 2 lammps_CT_CM.table LJLJ 12.0

pair_coeff 2 2 lammps_CM_CM.table LJLJ 12.0



## Parameters initialization

velocity 	all create 303.0 123456 dist gaussian



## Neighbor list settings

neigh_modify 	delay 0 every 1 check yes one 10000

neighbor 	12.0 bin



## Integrator

timestep 	1.0

run_style 	verlet



## Thermodynamics output

thermo 		100

thermo_style    custom step temp pe etotal press vol



## Set various fixes

#fix 		1 all bocs temp 303.0 303.0 100.0 cgiso 0.986 0.986 1000.0 analytic 296811.5 3600 2 84177.42 -101579.68 0.0

fix             1 all bocs temp 303.0 303.0 100.0 cgiso 0.986 0.986 1000.0 analytic delta_Fv.dat

# This makes lammps print the CG-P pressure rather than the raw pressure

thermo_modify press 1_press



## Run

run 1000

examples/USER/bocs/tests/cgheptaneFileSet/cgheptane.badFvData.lmp

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## Parameters initialization



units 		real

atom_style 	full



pair_style	table linear 1000

bond_style      table linear 1000

angle_style     table linear 1000

dihedral_style  none

improper_style  none

kspace_style    none



boundary 	p p p

dimension 	3

newton 		on



read_data	data.cgheptane



pair_coeff 1 1 lammps_CT_CT.table LJLJ 12.0

pair_coeff 1 2 lammps_CT_CM.table LJLJ 12.0

pair_coeff 2 2 lammps_CM_CM.table LJLJ 12.0



## Parameters initialization

velocity 	all create 303.0 123456 dist gaussian



## Neighbor list settings

neigh_modify 	delay 0 every 1 check yes one 10000

neighbor 	12.0 bin



## Integrator

timestep 	1.0

run_style 	verlet



## Thermodynamics output

thermo 		100

thermo_style    custom step temp pe etotal press vol



## Set various fixes

#fix 		1 all bocs temp 303.0 303.0 100.0 cgiso 0.986 0.986 1000.0 analytic 296811.5 3600 2 84177.42 -101579.68 0.0

fix             1 all bocs temp 303.0 303.0 100.0 cgiso 0.986 0.986 1000.0 cubic_spline delta_Fv_badbad.dat

# This makes lammps print the CG-P pressure rather than the raw pressure

thermo_modify press 1_press



## Run

run 1000

examples/USER/bocs/tests/cgheptaneFileSet/cgheptane.badSplineDataFileName.lmp

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## Parameters initialization



units 		real

atom_style 	full



pair_style	table linear 1000

bond_style      table linear 1000

angle_style     table linear 1000

dihedral_style  none

improper_style  none

kspace_style    none



boundary 	p p p

dimension 	3

newton 		on



read_data	data.cgheptane



pair_coeff 1 1 lammps_CT_CT.table LJLJ 12.0

pair_coeff 1 2 lammps_CT_CM.table LJLJ 12.0

pair_coeff 2 2 lammps_CM_CM.table LJLJ 12.0



## Parameters initialization

velocity 	all create 303.0 123456 dist gaussian



## Neighbor list settings

neigh_modify 	delay 0 every 1 check yes one 10000

neighbor 	12.0 bin



## Integrator

timestep 	1.0

run_style 	verlet



## Thermodynamics output

thermo 		100

thermo_style    custom step temp pe etotal press vol



## Set various fixes

#fix 		1 all bocs temp 303.0 303.0 100.0 cgiso 0.986 0.986 1000.0 analytic 296811.5 3600 2 84177.42 -101579.68 0.0

fix             1 all bocs temp 303.0 303.0 100.0 cgiso 0.986 0.986 1000.0 cubic_spline bad_file_name.dat

# This makes lammps print the CG-P pressure rather than the raw pressure

thermo_modify press 1_press



## Run

run 1000

examples/USER/bocs/tests/cgheptaneFileSet/cgheptane.cubic200.lmp

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## Parameters initialization



units 		real

atom_style 	full



pair_style	table linear 1000

bond_style      table linear 1000

angle_style     table linear 1000

dihedral_style  none

improper_style  none

kspace_style    none



boundary 	p p p

dimension 	3

newton 		on



read_data	data.cgheptane



pair_coeff 1 1 lammps_CT_CT.table LJLJ 12.0

pair_coeff 1 2 lammps_CT_CM.table LJLJ 12.0

pair_coeff 2 2 lammps_CM_CM.table LJLJ 12.0



## Parameters initialization

velocity 	all create 303.0 123456 dist gaussian



## Neighbor list settings

neigh_modify 	delay 0 every 1 check yes one 10000

neighbor 	12.0 bin



## Integrator

timestep 	1.0

run_style 	verlet



## Thermodynamics output

thermo 		100

thermo_style    custom step temp pe etotal press vol



## Set various fixes

#fix 		1 all bocs temp 303.0 303.0 100.0 cgiso 0.986 0.986 1000.0 analytic 296811.5 3600 2 84177.42 -101579.68 0.0

fix             1 all bocs temp 303.0 303.0 100.0 cgiso 0.986 0.986 1000.0 cubic_spline delta_Fv.dat

# This makes lammps print the CG-P pressure rather than the raw pressure

thermo_modify press 1_press



## Run

run 200

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