Gromacs
2025-dev-20240913-b871546
Main Page
Modules
Other Docs
Namespaces
Classes
Files
Examples
All
Classes
Namespaces
Files
Functions
Variables
Typedefs
Enumerations
Enumerator
Friends
Macros
Groups
Pages
src
gromacs
mdlib
mdlib → api Relation
File in src/gromacs/mdlib
Includes file in api
boxdeformation.cpp
legacy
/
include
/
gromacs
/
utility
/
arrayref.h
boxdeformation.cpp
legacy
/
include
/
gromacs
/
utility
/
exceptions.h
boxdeformation.cpp
legacy
/
include
/
gromacs
/
mdtypes
/
md_enums.h
boxdeformation.cpp
legacy
/
include
/
gromacs
/
utility
/
real.h
boxdeformation.h
legacy
/
include
/
gromacs
/
utility
/
basedefinitions.h
boxdeformation.h
legacy
/
include
/
gromacs
/
utility
/
classhelpers.h
broadcaststructs.cpp
legacy
/
include
/
gromacs
/
utility
/
arrayref.h
broadcaststructs.cpp
legacy
/
include
/
gromacs
/
utility
/
enumerationhelpers.h
broadcaststructs.cpp
legacy
/
include
/
gromacs
/
utility
/
gmxassert.h
broadcaststructs.cpp
legacy
/
include
/
gromacs
/
mdtypes
/
md_enums.h
broadcaststructs.h
legacy
/
include
/
gromacs
/
utility
/
smalloc.h
tests
/
calc_verletbuf.cpp
legacy
/
include
/
gromacs
/
utility
/
arrayref.h
calc_verletbuf.cpp
legacy
/
include
/
gromacs
/
utility
/
arrayref.h
tests
/
calc_verletbuf.cpp
legacy
/
include
/
gromacs
/
utility
/
basedefinitions.h
tests
/
calc_verletbuf.cpp
legacy
/
include
/
gromacs
/
math
/
functions.h
calc_verletbuf.cpp
legacy
/
include
/
gromacs
/
math
/
functions.h
tests
/
calc_verletbuf.cpp
legacy
/
include
/
gromacs
/
utility
/
gmxassert.h
calc_verletbuf.cpp
legacy
/
include
/
gromacs
/
topology
/
idef.h
calc_verletbuf.cpp
legacy
/
include
/
gromacs
/
topology
/
ifunc.h
calc_verletbuf.cpp
legacy
/
include
/
gromacs
/
mdtypes
/
md_enums.h
tests
/
calc_verletbuf.cpp
legacy
/
include
/
gromacs
/
utility
/
real.h
calc_verletbuf.cpp
legacy
/
include
/
gromacs
/
utility
/
real.h
calc_verletbuf.h
legacy
/
include
/
gromacs
/
utility
/
basedefinitions.h
calc_verletbuf.h
legacy
/
include
/
gromacs
/
utility
/
gmxassert.h
calc_verletbuf.h
legacy
/
include
/
gromacs
/
utility
/
real.h
calcmu.cpp
legacy
/
include
/
gromacs
/
utility
/
arrayref.h
calcmu.h
legacy
/
include
/
gromacs
/
utility
/
basedefinitions.h
calcmu.h
legacy
/
include
/
gromacs
/
utility
/
real.h
calcvir.cpp
legacy
/
include
/
gromacs
/
utility
/
basedefinitions.h
calcvir.cpp
legacy
/
include
/
gromacs
/
utility
/
gmxassert.h
calcvir.cpp
legacy
/
include
/
gromacs
/
utility
/
real.h
checkpointhandler.cpp
legacy
/
include
/
gromacs
/
utility
/
gmxassert.h
checkpointhandler.h
legacy
/
include
/
gromacs
/
utility
/
real.h
compute_io.cpp
legacy
/
include
/
gromacs
/
utility
/
enumerationhelpers.h
compute_io.cpp
legacy
/
include
/
gromacs
/
math
/
functions.h
compute_io.cpp
legacy
/
include
/
gromacs
/
mdtypes
/
md_enums.h
compute_io.cpp
legacy
/
include
/
gromacs
/
utility
/
real.h
constr.cpp
legacy
/
include
/
gromacs
/
utility
/
arrayref.h
tests
/
constr.cpp
legacy
/
include
/
gromacs
/
utility
/
basedefinitions.h
constr.cpp
legacy
/
include
/
gromacs
/
utility
/
basedefinitions.h
tests
/
constr.cpp
legacy
/
include
/
gromacs
/
utility
/
enumerationhelpers.h
constr.cpp
legacy
/
include
/
gromacs
/
utility
/
enumerationhelpers.h
constr.cpp
legacy
/
include
/
gromacs
/
utility
/
exceptions.h
constr.cpp
legacy
/
include
/
gromacs
/
utility
/
gmxassert.h
constr.cpp
legacy
/
include
/
gromacs
/
topology
/
ifunc.h
constr.cpp
legacy
/
include
/
gromacs
/
utility
/
listoflists.h
tests
/
constr.cpp
legacy
/
include
/
gromacs
/
mdtypes
/
md_enums.h
constr.cpp
legacy
/
include
/
gromacs
/
mdtypes
/
md_enums.h
constr.cpp
legacy
/
include
/
gromacs
/
utility
/
pleasecite.h
tests
/
constr.cpp
legacy
/
include
/
gromacs
/
utility
/
real.h
constr.cpp
legacy
/
include
/
gromacs
/
utility
/
smalloc.h
tests
/
constr.cpp
legacy
/
include
/
gromacs
/
utility
/
stringutil.h
constr.h
legacy
/
include
/
gromacs
/
utility
/
arrayref.h
constr.h
legacy
/
include
/
gromacs
/
topology
/
idef.h
constr.h
legacy
/
include
/
gromacs
/
utility
/
real.h
constraint_gpu_helpers.cpp
legacy
/
include
/
gromacs
/
utility
/
arrayref.h
constraint_gpu_helpers.cpp
legacy
/
include
/
gromacs
/
utility
/
gmxassert.h
constraint_gpu_helpers.cpp
legacy
/
include
/
gromacs
/
topology
/
idef.h
constraint_gpu_helpers.cpp
legacy
/
include
/
gromacs
/
topology
/
ifunc.h
constraint_gpu_helpers.cpp
legacy
/
include
/
gromacs
/
utility
/
listoflists.h
constraint_gpu_helpers.h
legacy
/
include
/
gromacs
/
utility
/
arrayref.h
constraint_gpu_helpers.h
legacy
/
include
/
gromacs
/
utility
/
listoflists.h
constraint_gpu_helpers.h
legacy
/
include
/
gromacs
/
utility
/
real.h
constraintrange.cpp
legacy
/
include
/
gromacs
/
utility
/
arrayref.h
constraintrange.cpp
legacy
/
include
/
gromacs
/
utility
/
basedefinitions.h
constraintrange.cpp
legacy
/
include
/
gromacs
/
topology
/
idef.h
constraintrange.cpp
legacy
/
include
/
gromacs
/
topology
/
ifunc.h
constraintrange.cpp
legacy
/
include
/
gromacs
/
utility
/
listoflists.h
constraintrange.cpp
legacy
/
include
/
gromacs
/
mdtypes
/
md_enums.h
constraintrange.cpp
legacy
/
include
/
gromacs
/
utility
/
real.h
constraintrange.h
legacy
/
include
/
gromacs
/
utility
/
real.h
tests
/
constrtestdata.cpp
legacy
/
include
/
gromacs
/
mdtypes
/
md_enums.h
tests
/
constrtestdata.cpp
legacy
/
include
/
gromacs
/
utility
/
smalloc.h
tests
/
constrtestdata.cpp
legacy
/
include
/
gromacs
/
utility
/
stringutil.h
tests
/
constrtestdata.h
legacy
/
include
/
gromacs
/
utility
/
basedefinitions.h
tests
/
constrtestdata.h
legacy
/
include
/
gromacs
/
topology
/
idef.h
tests
/
constrtestdata.h
legacy
/
include
/
gromacs
/
topology
/
ifunc.h
tests
/
constrtestdata.h
legacy
/
include
/
gromacs
/
utility
/
real.h
tests
/
constrtestrunners.cpp
legacy
/
include
/
gromacs
/
utility
/
arrayref.h
tests
/
constrtestrunners.cpp
legacy
/
include
/
gromacs
/
topology
/
idef.h
tests
/
constrtestrunners.cpp
legacy
/
include
/
gromacs
/
topology
/
ifunc.h
tests
/
constrtestrunners.cpp
legacy
/
include
/
gromacs
/
utility
/
listoflists.h
tests
/
constrtestrunners.cpp
legacy
/
include
/
gromacs
/
mdtypes
/
md_enums.h
tests
/
constrtestrunners.cpp
legacy
/
include
/
gromacs
/
utility
/
unique_cptr.h
tests
/
constrtestrunners_gpu.cpp
legacy
/
include
/
gromacs
/
utility
/
basedefinitions.h
coupling.cpp
legacy
/
include
/
gromacs
/
utility
/
arrayref.h
coupling.cpp
legacy
/
include
/
gromacs
/
utility
/
basedefinitions.h
coupling.cpp
legacy
/
include
/
gromacs
/
math
/
functions.h
coupling.cpp
legacy
/
include
/
gromacs
/
utility
/
gmxassert.h
coupling.cpp
legacy
/
include
/
gromacs
/
topology
/
ifunc.h
coupling.cpp
legacy
/
include
/
gromacs
/
mdtypes
/
md_enums.h
coupling.cpp
legacy
/
include
/
gromacs
/
utility
/
pleasecite.h
coupling.cpp
legacy
/
include
/
gromacs
/
utility
/
smalloc.h
coupling.cpp
legacy
/
include
/
gromacs
/
utility
/
stringutil.h
coupling.h
legacy
/
include
/
gromacs
/
utility
/
enumerationhelpers.h
coupling.h
legacy
/
include
/
gromacs
/
mdtypes
/
md_enums.h
coupling.h
legacy
/
include
/
gromacs
/
utility
/
real.h
dispersioncorrection.cpp
legacy
/
include
/
gromacs
/
utility
/
arrayref.h
dispersioncorrection.cpp
legacy
/
include
/
gromacs
/
utility
/
basedefinitions.h
dispersioncorrection.cpp
legacy
/
include
/
gromacs
/
math
/
functions.h
dispersioncorrection.cpp
legacy
/
include
/
gromacs
/
utility
/
gmxassert.h
dispersioncorrection.cpp
legacy
/
include
/
gromacs
/
topology
/
idef.h
dispersioncorrection.cpp
legacy
/
include
/
gromacs
/
utility
/
listoflists.h
dispersioncorrection.cpp
legacy
/
include
/
gromacs
/
mdtypes
/
md_enums.h
dispersioncorrection.cpp
legacy
/
include
/
gromacs
/
utility
/
stringutil.h
dispersioncorrection.h
legacy
/
include
/
gromacs
/
utility
/
real.h
ebin.cpp
legacy
/
include
/
gromacs
/
utility
/
arrayref.h
tests
/
ebin.cpp
legacy
/
include
/
gromacs
/
utility
/
basedefinitions.h
ebin.cpp
legacy
/
include
/
gromacs
/
utility
/
basedefinitions.h
ebin.cpp
legacy
/
include
/
gromacs
/
utility
/
gmxassert.h
ebin.cpp
legacy
/
include
/
gromacs
/
topology
/
ifunc.h
tests
/
ebin.cpp
legacy
/
include
/
gromacs
/
utility
/
real.h
ebin.cpp
legacy
/
include
/
gromacs
/
utility
/
smalloc.h
ebin.cpp
legacy
/
include
/
gromacs
/
utility
/
stringutil.h
tests
/
ebin.cpp
legacy
/
include
/
gromacs
/
utility
/
unique_cptr.h
ebin.h
legacy
/
include
/
gromacs
/
utility
/
basedefinitions.h
ebin.h
legacy
/
include
/
gromacs
/
utility
/
real.h
enerdata_utils.cpp
legacy
/
include
/
gromacs
/
utility
/
basedefinitions.h
enerdata_utils.cpp
legacy
/
include
/
gromacs
/
utility
/
enumerationhelpers.h
enerdata_utils.cpp
legacy
/
include
/
gromacs
/
utility
/
gmxassert.h
enerdata_utils.cpp
legacy
/
include
/
gromacs
/
topology
/
ifunc.h
enerdata_utils.cpp
legacy
/
include
/
gromacs
/
mdtypes
/
md_enums.h
enerdata_utils.h
legacy
/
include
/
gromacs
/
utility
/
arrayref.h
enerdata_utils.h
legacy
/
include
/
gromacs
/
utility
/
real.h
energydrifttracker.cpp
legacy
/
include
/
gromacs
/
utility
/
gmxassert.h
tests
/
energydrifttracker.cpp
legacy
/
include
/
gromacs
/
utility
/
real.h
energydrifttracker.cpp
legacy
/
include
/
gromacs
/
utility
/
real.h
energydrifttracker.cpp
legacy
/
include
/
gromacs
/
utility
/
stringutil.h
energydrifttracker.h
legacy
/
include
/
gromacs
/
utility
/
real.h
tests
/
energyoutput.cpp
legacy
/
include
/
gromacs
/
utility
/
arrayref.h
tests
/
energyoutput.cpp
legacy
/
include
/
gromacs
/
utility
/
basedefinitions.h
energyoutput.cpp
legacy
/
include
/
gromacs
/
utility
/
basedefinitions.h
tests
/
energyoutput.cpp
legacy
/
include
/
gromacs
/
utility
/
enumerationhelpers.h
energyoutput.cpp
legacy
/
include
/
gromacs
/
utility
/
enumerationhelpers.h
energyoutput.cpp
legacy
/
include
/
gromacs
/
math
/
functions.h
energyoutput.cpp
legacy
/
include
/
gromacs
/
utility
/
gmxassert.h
tests
/
energyoutput.cpp
legacy
/
include
/
gromacs
/
topology
/
idef.h
tests
/
energyoutput.cpp
legacy
/
include
/
gromacs
/
topology
/
ifunc.h
tests
/
energyoutput.cpp
legacy
/
include
/
gromacs
/
mdtypes
/
md_enums.h
energyoutput.cpp
legacy
/
include
/
gromacs
/
mdtypes
/
md_enums.h
tests
/
energyoutput.cpp
legacy
/
include
/
gromacs
/
utility
/
real.h
tests
/
energyoutput.cpp
legacy
/
include
/
gromacs
/
utility
/
smalloc.h
energyoutput.cpp
legacy
/
include
/
gromacs
/
utility
/
smalloc.h
tests
/
energyoutput.cpp
legacy
/
include
/
gromacs
/
utility
/
stringutil.h
energyoutput.cpp
legacy
/
include
/
gromacs
/
utility
/
stringutil.h
tests
/
energyoutput.cpp
legacy
/
include
/
gromacs
/
utility
/
unique_cptr.h
energyoutput.h
legacy
/
include
/
gromacs
/
utility
/
arrayref.h
energyoutput.h
legacy
/
include
/
gromacs
/
utility
/
enumerationhelpers.h
energyoutput.h
legacy
/
include
/
gromacs
/
topology
/
ifunc.h
energyoutput.h
legacy
/
include
/
gromacs
/
mdtypes
/
md_enums.h
energyoutput.h
legacy
/
include
/
gromacs
/
utility
/
real.h
expanded.cpp
legacy
/
include
/
gromacs
/
utility
/
arrayref.h
expanded.cpp
legacy
/
include
/
gromacs
/
utility
/
basedefinitions.h
tests
/
expanded.cpp
legacy
/
include
/
gromacs
/
utility
/
enumerationhelpers.h
expanded.cpp
legacy
/
include
/
gromacs
/
utility
/
enumerationhelpers.h
tests
/
expanded.cpp
legacy
/
include
/
gromacs
/
utility
/
exceptions.h
expanded.cpp
legacy
/
include
/
gromacs
/
math
/
functions.h
expanded.cpp
legacy
/
include
/
gromacs
/
utility
/
gmxassert.h
expanded.cpp
legacy
/
include
/
gromacs
/
topology
/
ifunc.h
tests
/
expanded.cpp
legacy
/
include
/
gromacs
/
mdtypes
/
md_enums.h
expanded.cpp
legacy
/
include
/
gromacs
/
mdtypes
/
md_enums.h
tests
/
expanded.cpp
legacy
/
include
/
gromacs
/
utility
/
real.h
expanded.cpp
legacy
/
include
/
gromacs
/
utility
/
real.h
expanded.cpp
legacy
/
include
/
gromacs
/
utility
/
smalloc.h
expanded_internal.cpp
legacy
/
include
/
gromacs
/
utility
/
exceptions.h
expanded_internal.cpp
legacy
/
include
/
gromacs
/
mdtypes
/
md_enums.h
expanded_internal.h
legacy
/
include
/
gromacs
/
utility
/
real.h
force.cpp
legacy
/
include
/
gromacs
/
utility
/
basedefinitions.h
force.cpp
legacy
/
include
/
gromacs
/
utility
/
exceptions.h
force.cpp
legacy
/
include
/
gromacs
/
utility
/
gmxassert.h
force.cpp
legacy
/
include
/
gromacs
/
topology
/
ifunc.h
force.cpp
legacy
/
include
/
gromacs
/
mdtypes
/
md_enums.h
force.h
legacy
/
include
/
gromacs
/
utility
/
arrayref.h
force.h
legacy
/
include
/
gromacs
/
utility
/
enumerationhelpers.h
force.h
legacy
/
include
/
gromacs
/
mdtypes
/
md_enums.h
force.h
legacy
/
include
/
gromacs
/
utility
/
real.h
forcerec.cpp
legacy
/
include
/
gromacs
/
utility
/
basedefinitions.h
forcerec.cpp
legacy
/
include
/
gromacs
/
utility
/
enumerationhelpers.h
forcerec.cpp
legacy
/
include
/
gromacs
/
utility
/
exceptions.h
forcerec.cpp
legacy
/
include
/
gromacs
/
math
/
functions.h
forcerec.cpp
legacy
/
include
/
gromacs
/
utility
/
gmxassert.h
forcerec.cpp
legacy
/
include
/
gromacs
/
topology
/
idef.h
forcerec.cpp
legacy
/
include
/
gromacs
/
topology
/
ifunc.h
forcerec.cpp
legacy
/
include
/
gromacs
/
utility
/
listoflists.h
forcerec.cpp
legacy
/
include
/
gromacs
/
mdtypes
/
md_enums.h
forcerec.cpp
legacy
/
include
/
gromacs
/
utility
/
pleasecite.h
forcerec.cpp
legacy
/
include
/
gromacs
/
utility
/
smalloc.h
forcerec.cpp
legacy
/
include
/
gromacs
/
utility
/
stringutil.h
forcerec.h
legacy
/
include
/
gromacs
/
utility
/
arrayref.h
forcerec.h
legacy
/
include
/
gromacs
/
utility
/
real.h
tests
/
freeenergyparameters.cpp
legacy
/
include
/
gromacs
/
utility
/
arrayref.h
freeenergyparameters.cpp
legacy
/
include
/
gromacs
/
utility
/
arrayref.h
tests
/
freeenergyparameters.cpp
legacy
/
include
/
gromacs
/
utility
/
enumerationhelpers.h
freeenergyparameters.cpp
legacy
/
include
/
gromacs
/
utility
/
enumerationhelpers.h
tests
/
freeenergyparameters.cpp
legacy
/
include
/
gromacs
/
utility
/
real.h
freeenergyparameters.h
legacy
/
include
/
gromacs
/
utility
/
enumerationhelpers.h
freeenergyparameters.h
legacy
/
include
/
gromacs
/
mdtypes
/
md_enums.h
freeenergyparameters.h
legacy
/
include
/
gromacs
/
utility
/
real.h
gmx_omp_nthreads.cpp
legacy
/
include
/
gromacs
/
utility
/
enumerationhelpers.h
gmx_omp_nthreads.cpp
legacy
/
include
/
gromacs
/
utility
/
gmxassert.h
gmx_omp_nthreads.cpp
legacy
/
include
/
gromacs
/
utility
/
programcontext.h
gmx_omp_nthreads.h
legacy
/
include
/
gromacs
/
utility
/
basedefinitions.h
gpuforcereduction.h
legacy
/
include
/
gromacs
/
utility
/
arrayref.h
gpuforcereduction_impl.cpp
legacy
/
include
/
gromacs
/
utility
/
gmxassert.h
gpuforcereduction_impl_stubs.cpp
legacy
/
include
/
gromacs
/
utility
/
arrayref.h
gpuforcereduction_impl_stubs.cpp
legacy
/
include
/
gromacs
/
utility
/
gmxassert.h
groupcoord.cpp
legacy
/
include
/
gromacs
/
utility
/
gmxassert.h
groupcoord.cpp
legacy
/
include
/
gromacs
/
utility
/
smalloc.h
groupcoord.h
legacy
/
include
/
gromacs
/
utility
/
basedefinitions.h
groupcoord.h
legacy
/
include
/
gromacs
/
utility
/
real.h
tests
/
langevin.cpp
legacy
/
include
/
gromacs
/
utility
/
real.h
tests
/
langevin.cpp
legacy
/
include
/
gromacs
/
utility
/
stringutil.h
tests
/
langevintestdata.cpp
legacy
/
include
/
gromacs
/
utility
/
arrayref.h
tests
/
langevintestdata.cpp
legacy
/
include
/
gromacs
/
utility
/
gmxassert.h
tests
/
langevintestdata.cpp
legacy
/
include
/
gromacs
/
mdtypes
/
md_enums.h
tests
/
langevintestdata.cpp
legacy
/
include
/
gromacs
/
utility
/
smalloc.h
tests
/
langevintestdata.h
legacy
/
include
/
gromacs
/
utility
/
real.h
tests
/
langevintestrunners.cpp
legacy
/
include
/
gromacs
/
utility
/
arrayref.h
tests
/
langevintestrunners.cpp
legacy
/
include
/
gromacs
/
mdtypes
/
md_enums.h
tests
/
leapfrog.cpp
legacy
/
include
/
gromacs
/
utility
/
real.h
tests
/
leapfrog.cpp
legacy
/
include
/
gromacs
/
utility
/
stringutil.h
leapfrog_gpu.cpp
legacy
/
include
/
gromacs
/
utility
/
arrayref.h
leapfrog_gpu.h
legacy
/
include
/
gromacs
/
utility
/
arrayref.h
leapfrog_gpu_internal_sycl.cpp
legacy
/
include
/
gromacs
/
utility
/
arrayref.h
tests
/
leapfrogtestdata.cpp
legacy
/
include
/
gromacs
/
utility
/
arrayref.h
tests
/
leapfrogtestdata.cpp
legacy
/
include
/
gromacs
/
mdtypes
/
md_enums.h
tests
/
leapfrogtestdata.cpp
legacy
/
include
/
gromacs
/
utility
/
smalloc.h
tests
/
leapfrogtestdata.cpp
legacy
/
include
/
gromacs
/
utility
/
stringutil.h
tests
/
leapfrogtestdata.h
legacy
/
include
/
gromacs
/
utility
/
real.h
tests
/
leapfrogtestdata.h
legacy
/
include
/
gromacs
/
utility
/
stringutil.h
tests
/
leapfrogtestrunners.cpp
legacy
/
include
/
gromacs
/
utility
/
arrayref.h
tests
/
leapfrogtestrunners.cpp
legacy
/
include
/
gromacs
/
mdtypes
/
md_enums.h
tests
/
leapfrogtestrunners_gpu.cpp
legacy
/
include
/
gromacs
/
utility
/
basedefinitions.h
lincs.cpp
legacy
/
include
/
gromacs
/
utility
/
arrayref.h
lincs.cpp
legacy
/
include
/
gromacs
/
utility
/
basedefinitions.h
lincs.cpp
legacy
/
include
/
gromacs
/
utility
/
exceptions.h
lincs.cpp
legacy
/
include
/
gromacs
/
math
/
functions.h
lincs.cpp
legacy
/
include
/
gromacs
/
topology
/
idef.h
lincs.cpp
legacy
/
include
/
gromacs
/
topology
/
ifunc.h
lincs.cpp
legacy
/
include
/
gromacs
/
utility
/
listoflists.h
lincs.cpp
legacy
/
include
/
gromacs
/
mdtypes
/
md_enums.h
lincs.cpp
legacy
/
include
/
gromacs
/
utility
/
pleasecite.h
lincs.cpp
legacy
/
include
/
gromacs
/
utility
/
stringutil.h
lincs.h
legacy
/
include
/
gromacs
/
utility
/
arrayref.h
lincs.h
legacy
/
include
/
gromacs
/
utility
/
basedefinitions.h
lincs.h
legacy
/
include
/
gromacs
/
utility
/
real.h
lincs_gpu.cpp
legacy
/
include
/
gromacs
/
math
/
functions.h
lincs_gpu.cpp
legacy
/
include
/
gromacs
/
topology
/
ifunc.h
lincs_gpu.cpp
legacy
/
include
/
gromacs
/
utility
/
listoflists.h
lincs_gpu_internal_sycl.cpp
legacy
/
include
/
gromacs
/
utility
/
gmxassert.h
makeconstraints.h
legacy
/
include
/
gromacs
/
topology
/
ifunc.h
md_support.cpp
legacy
/
include
/
gromacs
/
utility
/
arrayref.h
md_support.cpp
legacy
/
include
/
gromacs
/
utility
/
enumerationhelpers.h
md_support.cpp
legacy
/
include
/
gromacs
/
utility
/
gmxassert.h
md_support.cpp
legacy
/
include
/
gromacs
/
topology
/
ifunc.h
md_support.cpp
legacy
/
include
/
gromacs
/
mdtypes
/
md_enums.h
md_support.cpp
legacy
/
include
/
gromacs
/
utility
/
real.h
md_support.cpp
legacy
/
include
/
gromacs
/
utility
/
smalloc.h
md_support.h
legacy
/
include
/
gromacs
/
utility
/
basedefinitions.h
md_support.h
legacy
/
include
/
gromacs
/
mdtypes
/
md_enums.h
mdatoms.cpp
legacy
/
include
/
gromacs
/
utility
/
arrayref.h
mdatoms.cpp
legacy
/
include
/
gromacs
/
utility
/
basedefinitions.h
mdatoms.cpp
legacy
/
include
/
gromacs
/
utility
/
enumerationhelpers.h
mdatoms.cpp
legacy
/
include
/
gromacs
/
utility
/
exceptions.h
mdatoms.cpp
legacy
/
include
/
gromacs
/
math
/
functions.h
mdatoms.cpp
legacy
/
include
/
gromacs
/
utility
/
gmxassert.h
mdatoms.cpp
legacy
/
include
/
gromacs
/
topology
/
idef.h
mdatoms.cpp
legacy
/
include
/
gromacs
/
topology
/
ifunc.h
mdatoms.cpp
legacy
/
include
/
gromacs
/
mdtypes
/
md_enums.h
mdatoms.cpp
legacy
/
include
/
gromacs
/
utility
/
smalloc.h
mdatoms.h
legacy
/
include
/
gromacs
/
utility
/
real.h
mdatoms.h
legacy
/
include
/
gromacs
/
utility
/
unique_cptr.h
mdebin_bar.cpp
legacy
/
include
/
gromacs
/
utility
/
arrayref.h
mdebin_bar.cpp
legacy
/
include
/
gromacs
/
utility
/
basedefinitions.h
mdebin_bar.cpp
legacy
/
include
/
gromacs
/
utility
/
enumerationhelpers.h
mdebin_bar.cpp
legacy
/
include
/
gromacs
/
utility
/
gmxassert.h
mdebin_bar.cpp
legacy
/
include
/
gromacs
/
mdtypes
/
md_enums.h
mdebin_bar.cpp
legacy
/
include
/
gromacs
/
utility
/
smalloc.h
mdebin_bar.h
legacy
/
include
/
gromacs
/
utility
/
real.h
mdgraph_gpu.h
legacy
/
include
/
gromacs
/
utility
/
gmxassert.h
mdgraph_gpu.h
legacy
/
include
/
gromacs
/
mdtypes
/
md_enums.h
mdgraph_gpu_impl.cpp
legacy
/
include
/
gromacs
/
utility
/
classhelpers.h
mdgraph_gpu_impl.cpp
legacy
/
include
/
gromacs
/
utility
/
gmxassert.h
mdoutf.cpp
legacy
/
include
/
gromacs
/
utility
/
baseversion.h
mdoutf.cpp
legacy
/
include
/
gromacs
/
utility
/
enumerationhelpers.h
mdoutf.cpp
legacy
/
include
/
gromacs
/
utility
/
exceptions.h
mdoutf.cpp
legacy
/
include
/
gromacs
/
utility
/
futil.h
mdoutf.cpp
legacy
/
include
/
gromacs
/
utility
/
gmxassert.h
mdoutf.cpp
legacy
/
include
/
gromacs
/
mdtypes
/
md_enums.h
mdoutf.cpp
legacy
/
include
/
gromacs
/
utility
/
pleasecite.h
mdoutf.cpp
legacy
/
include
/
gromacs
/
utility
/
programcontext.h
mdoutf.cpp
legacy
/
include
/
gromacs
/
utility
/
real.h
mdoutf.cpp
legacy
/
include
/
gromacs
/
utility
/
smalloc.h
mdoutf.cpp
legacy
/
include
/
gromacs
/
utility
/
stringutil.h
mdoutf.h
legacy
/
include
/
gromacs
/
utility
/
arrayref.h
mdoutf.h
legacy
/
include
/
gromacs
/
utility
/
basedefinitions.h
membed.cpp
legacy
/
include
/
gromacs
/
utility
/
arrayref.h
membed.cpp
legacy
/
include
/
gromacs
/
utility
/
basedefinitions.h
membed.cpp
legacy
/
include
/
gromacs
/
utility
/
enumerationhelpers.h
membed.cpp
legacy
/
include
/
gromacs
/
utility
/
exceptions.h
membed.cpp
legacy
/
include
/
gromacs
/
utility
/
futil.h
membed.cpp
legacy
/
include
/
gromacs
/
topology
/
idef.h
membed.cpp
legacy
/
include
/
gromacs
/
topology
/
ifunc.h
membed.cpp
legacy
/
include
/
gromacs
/
mdtypes
/
md_enums.h
membed.cpp
legacy
/
include
/
gromacs
/
utility
/
smalloc.h
membed.cpp
legacy
/
include
/
gromacs
/
utility
/
stringutil.h
membed.h
legacy
/
include
/
gromacs
/
utility
/
real.h
tests
/
parrinellorahman.cpp
legacy
/
include
/
gromacs
/
utility
/
enumerationhelpers.h
tests
/
parrinellorahman.cpp
legacy
/
include
/
gromacs
/
mdtypes
/
md_enums.h
tests
/
parrinellorahman.cpp
legacy
/
include
/
gromacs
/
utility
/
real.h
tests
/
parrinellorahman.cpp
legacy
/
include
/
gromacs
/
utility
/
stringutil.h
perf_est.cpp
legacy
/
include
/
gromacs
/
utility
/
arrayref.h
perf_est.cpp
legacy
/
include
/
gromacs
/
math
/
functions.h
perf_est.cpp
legacy
/
include
/
gromacs
/
topology
/
idef.h
perf_est.cpp
legacy
/
include
/
gromacs
/
topology
/
ifunc.h
perf_est.cpp
legacy
/
include
/
gromacs
/
utility
/
listoflists.h
perf_est.cpp
legacy
/
include
/
gromacs
/
mdtypes
/
md_enums.h
perf_est.cpp
legacy
/
include
/
gromacs
/
utility
/
real.h
perf_est.h
legacy
/
include
/
gromacs
/
utility
/
basedefinitions.h
rbin.cpp
legacy
/
include
/
gromacs
/
utility
/
arrayref.h
rbin.cpp
legacy
/
include
/
gromacs
/
utility
/
smalloc.h
rbin.h
legacy
/
include
/
gromacs
/
utility
/
arrayref.h
rbin.h
legacy
/
include
/
gromacs
/
utility
/
real.h
resethandler.cpp
legacy
/
include
/
gromacs
/
utility
/
gmxassert.h
resethandler.h
legacy
/
include
/
gromacs
/
utility
/
real.h
rf_util.cpp
legacy
/
include
/
gromacs
/
math
/
functions.h
rf_util.cpp
legacy
/
include
/
gromacs
/
mdtypes
/
md_enums.h
rf_util.cpp
legacy
/
include
/
gromacs
/
utility
/
pleasecite.h
rf_util.h
legacy
/
include
/
gromacs
/
utility
/
real.h
settle.cpp
legacy
/
include
/
gromacs
/
utility
/
arrayref.h
settle.cpp
legacy
/
include
/
gromacs
/
utility
/
basedefinitions.h
settle.cpp
legacy
/
include
/
gromacs
/
math
/
functions.h
settle.cpp
legacy
/
include
/
gromacs
/
utility
/
gmxassert.h
tests
/
settle.cpp
legacy
/
include
/
gromacs
/
topology
/
idef.h
settle.cpp
legacy
/
include
/
gromacs
/
topology
/
idef.h
tests
/
settle.cpp
legacy
/
include
/
gromacs
/
topology
/
ifunc.h
settle.cpp
legacy
/
include
/
gromacs
/
topology
/
ifunc.h
tests
/
settle.cpp
legacy
/
include
/
gromacs
/
mdtypes
/
md_enums.h
settle.cpp
legacy
/
include
/
gromacs
/
mdtypes
/
md_enums.h
tests
/
settle.cpp
legacy
/
include
/
gromacs
/
utility
/
real.h
tests
/
settle.cpp
legacy
/
include
/
gromacs
/
utility
/
stringutil.h
tests
/
settle.cpp
legacy
/
include
/
gromacs
/
utility
/
unique_cptr.h
settle.h
legacy
/
include
/
gromacs
/
topology
/
idef.h
settle.h
legacy
/
include
/
gromacs
/
utility
/
real.h
settle_gpu.cpp
legacy
/
include
/
gromacs
/
math
/
functions.h
settle_gpu.h
legacy
/
include
/
gromacs
/
math
/
functions.h
settle_gpu_internal_sycl.cpp
legacy
/
include
/
gromacs
/
utility
/
gmxassert.h
tests
/
settletestdata.cpp
legacy
/
include
/
gromacs
/
topology
/
idef.h
tests
/
settletestdata.cpp
legacy
/
include
/
gromacs
/
topology
/
ifunc.h
tests
/
settletestdata.cpp
legacy
/
include
/
gromacs
/
utility
/
smalloc.h
tests
/
settletestdata.cpp
legacy
/
include
/
gromacs
/
utility
/
stringutil.h
tests
/
settletestdata.cpp
legacy
/
include
/
gromacs
/
utility
/
unique_cptr.h
tests
/
settletestdata.h
legacy
/
include
/
gromacs
/
topology
/
idef.h
tests
/
settletestdata.h
legacy
/
include
/
gromacs
/
topology
/
ifunc.h
tests
/
settletestdata.h
legacy
/
include
/
gromacs
/
utility
/
real.h
tests
/
settletestrunners.cpp
legacy
/
include
/
gromacs
/
utility
/
arrayref.h
tests
/
settletestrunners.cpp
legacy
/
include
/
gromacs
/
topology
/
idef.h
tests
/
settletestrunners.cpp
legacy
/
include
/
gromacs
/
topology
/
ifunc.h
tests
/
settletestrunners_gpu.cpp
legacy
/
include
/
gromacs
/
utility
/
basedefinitions.h
tests
/
shake.cpp
legacy
/
include
/
gromacs
/
utility
/
arrayref.h
shake.cpp
legacy
/
include
/
gromacs
/
utility
/
arrayref.h
tests
/
shake.cpp
legacy
/
include
/
gromacs
/
utility
/
basedefinitions.h
shake.cpp
legacy
/
include
/
gromacs
/
utility
/
basedefinitions.h
shake.cpp
legacy
/
include
/
gromacs
/
math
/
functions.h
shake.cpp
legacy
/
include
/
gromacs
/
utility
/
gmxassert.h
shake.cpp
legacy
/
include
/
gromacs
/
topology
/
idef.h
shake.cpp
legacy
/
include
/
gromacs
/
topology
/
ifunc.h
shake.cpp
legacy
/
include
/
gromacs
/
utility
/
listoflists.h
shake.cpp
legacy
/
include
/
gromacs
/
mdtypes
/
md_enums.h
tests
/
shake.cpp
legacy
/
include
/
gromacs
/
utility
/
real.h
shake.h
legacy
/
include
/
gromacs
/
utility
/
real.h
sighandler.cpp
legacy
/
include
/
gromacs
/
utility
/
enumerationhelpers.h
sighandler.cpp
legacy
/
include
/
gromacs
/
utility
/
exceptions.h
sighandler.h
legacy
/
include
/
gromacs
/
utility
/
basedefinitions.h
sim_util.cpp
legacy
/
include
/
gromacs
/
utility
/
arrayref.h
sim_util.cpp
legacy
/
include
/
gromacs
/
utility
/
basedefinitions.h
sim_util.cpp
legacy
/
include
/
gromacs
/
utility
/
enumerationhelpers.h
sim_util.cpp
legacy
/
include
/
gromacs
/
utility
/
exceptions.h
sim_util.cpp
legacy
/
include
/
gromacs
/
math
/
functions.h
sim_util.cpp
legacy
/
include
/
gromacs
/
utility
/
gmxassert.h
sim_util.cpp
legacy
/
include
/
gromacs
/
topology
/
ifunc.h
sim_util.cpp
legacy
/
include
/
gromacs
/
mdtypes
/
md_enums.h
sim_util.cpp
legacy
/
include
/
gromacs
/
utility
/
range.h
sim_util.cpp
legacy
/
include
/
gromacs
/
utility
/
real.h
sim_util.cpp
legacy
/
include
/
gromacs
/
utility
/
smalloc.h
sim_util.cpp
legacy
/
include
/
gromacs
/
utility
/
stringutil.h
tests
/
simulationsignal.cpp
legacy
/
include
/
gromacs
/
utility
/
arrayref.h
simulationsignal.cpp
legacy
/
include
/
gromacs
/
utility
/
arrayref.h
simulationsignal.cpp
legacy
/
include
/
gromacs
/
utility
/
gmxassert.h
simulationsignal.cpp
legacy
/
include
/
gromacs
/
utility
/
real.h
simulationsignal.h
legacy
/
include
/
gromacs
/
utility
/
real.h
splitter.cpp
legacy
/
include
/
gromacs
/
utility
/
arrayref.h
splitter.cpp
legacy
/
include
/
gromacs
/
utility
/
gmxassert.h
splitter.cpp
legacy
/
include
/
gromacs
/
topology
/
idef.h
splitter.cpp
legacy
/
include
/
gromacs
/
utility
/
listoflists.h
splitter.h
legacy
/
include
/
gromacs
/
utility
/
basedefinitions.h
stat.cpp
legacy
/
include
/
gromacs
/
utility
/
arrayref.h
stat.cpp
legacy
/
include
/
gromacs
/
utility
/
basedefinitions.h
stat.cpp
legacy
/
include
/
gromacs
/
utility
/
enumerationhelpers.h
stat.cpp
legacy
/
include
/
gromacs
/
utility
/
futil.h
stat.cpp
legacy
/
include
/
gromacs
/
topology
/
ifunc.h
stat.cpp
legacy
/
include
/
gromacs
/
mdtypes
/
md_enums.h
stat.cpp
legacy
/
include
/
gromacs
/
utility
/
smalloc.h
stat.h
legacy
/
include
/
gromacs
/
utility
/
real.h
stophandler.h
legacy
/
include
/
gromacs
/
utility
/
basedefinitions.h
stophandler.h
legacy
/
include
/
gromacs
/
utility
/
real.h
tgroup.h
legacy
/
include
/
gromacs
/
utility
/
real.h
trajectory_writing.cpp
legacy
/
include
/
gromacs
/
utility
/
arrayref.h
trajectory_writing.cpp
legacy
/
include
/
gromacs
/
utility
/
smalloc.h
trajectory_writing.h
legacy
/
include
/
gromacs
/
utility
/
basedefinitions.h
update.cpp
legacy
/
include
/
gromacs
/
utility
/
basedefinitions.h
update.cpp
legacy
/
include
/
gromacs
/
utility
/
enumerationhelpers.h
update.cpp
legacy
/
include
/
gromacs
/
utility
/
exceptions.h
update.cpp
legacy
/
include
/
gromacs
/
math
/
functions.h
update.cpp
legacy
/
include
/
gromacs
/
utility
/
futil.h
update.cpp
legacy
/
include
/
gromacs
/
utility
/
gmxassert.h
update.cpp
legacy
/
include
/
gromacs
/
mdtypes
/
md_enums.h
update.cpp
legacy
/
include
/
gromacs
/
utility
/
smalloc.h
update.h
legacy
/
include
/
gromacs
/
utility
/
arrayref.h
update.h
legacy
/
include
/
gromacs
/
mdtypes
/
md_enums.h
update.h
legacy
/
include
/
gromacs
/
utility
/
real.h
update_constrain_gpu.h
legacy
/
include
/
gromacs
/
utility
/
arrayref.h
update_constrain_gpu_impl_stubs.cpp
legacy
/
include
/
gromacs
/
utility
/
arrayref.h
update_constrain_gpu_impl_stubs.cpp
legacy
/
include
/
gromacs
/
utility
/
gmxassert.h
update_constrain_gpu_impl_stubs.cpp
legacy
/
include
/
gromacs
/
utility
/
real.h
update_constrain_gpu_internal_sycl.cpp
legacy
/
include
/
gromacs
/
utility
/
gmxassert.h
update_vv.cpp
legacy
/
include
/
gromacs
/
utility
/
arrayref.h
update_vv.cpp
legacy
/
include
/
gromacs
/
utility
/
basedefinitions.h
update_vv.cpp
legacy
/
include
/
gromacs
/
topology
/
ifunc.h
update_vv.cpp
legacy
/
include
/
gromacs
/
utility
/
smalloc.h
update_vv.h
legacy
/
include
/
gromacs
/
utility
/
enumerationhelpers.h
update_vv.h
legacy
/
include
/
gromacs
/
mdtypes
/
md_enums.h
update_vv.h
legacy
/
include
/
gromacs
/
utility
/
real.h
tests
/
updategroups.cpp
legacy
/
include
/
gromacs
/
utility
/
arrayref.h
updategroups.cpp
legacy
/
include
/
gromacs
/
utility
/
enumerationhelpers.h
updategroups.cpp
legacy
/
include
/
gromacs
/
math
/
functions.h
updategroups.cpp
legacy
/
include
/
gromacs
/
utility
/
gmxassert.h
tests
/
updategroups.cpp
legacy
/
include
/
gromacs
/
topology
/
idef.h
updategroups.cpp
legacy
/
include
/
gromacs
/
topology
/
idef.h
tests
/
updategroups.cpp
legacy
/
include
/
gromacs
/
topology
/
ifunc.h
updategroups.cpp
legacy
/
include
/
gromacs
/
topology
/
ifunc.h
updategroups.cpp
legacy
/
include
/
gromacs
/
utility
/
listoflists.h
tests
/
updategroups.cpp
legacy
/
include
/
gromacs
/
utility
/
real.h
updategroups.h
legacy
/
include
/
gromacs
/
utility
/
arrayref.h
updategroups.h
legacy
/
include
/
gromacs
/
utility
/
real.h
tests
/
updategroupscog.cpp
legacy
/
include
/
gromacs
/
utility
/
arrayref.h
updategroupscog.cpp
legacy
/
include
/
gromacs
/
utility
/
basedefinitions.h
tests
/
updategroupscog.cpp
legacy
/
include
/
gromacs
/
math
/
functions.h
tests
/
updategroupscog.cpp
legacy
/
include
/
gromacs
/
topology
/
idef.h
tests
/
updategroupscog.cpp
legacy
/
include
/
gromacs
/
topology
/
ifunc.h
tests
/
updategroupscog.cpp
legacy
/
include
/
gromacs
/
utility
/
real.h
updategroupscog.h
legacy
/
include
/
gromacs
/
utility
/
arrayref.h
updategroupscog.h
legacy
/
include
/
gromacs
/
utility
/
gmxassert.h
updategroupscog.h
legacy
/
include
/
gromacs
/
utility
/
real.h
vcm.cpp
legacy
/
include
/
gromacs
/
utility
/
arrayref.h
vcm.cpp
legacy
/
include
/
gromacs
/
utility
/
basedefinitions.h
vcm.cpp
legacy
/
include
/
gromacs
/
utility
/
enumerationhelpers.h
vcm.cpp
legacy
/
include
/
gromacs
/
math
/
functions.h
vcm.cpp
legacy
/
include
/
gromacs
/
utility
/
gmxassert.h
vcm.cpp
legacy
/
include
/
gromacs
/
mdtypes
/
md_enums.h
vcm.cpp
legacy
/
include
/
gromacs
/
utility
/
smalloc.h
vcm.h
legacy
/
include
/
gromacs
/
mdtypes
/
md_enums.h
vcm.h
legacy
/
include
/
gromacs
/
utility
/
real.h
vsite.cpp
legacy
/
include
/
gromacs
/
utility
/
arrayref.h
vsite.cpp
legacy
/
include
/
gromacs
/
utility
/
basedefinitions.h
vsite.cpp
legacy
/
include
/
gromacs
/
utility
/
exceptions.h
vsite.cpp
legacy
/
include
/
gromacs
/
math
/
functions.h
vsite.cpp
legacy
/
include
/
gromacs
/
utility
/
gmxassert.h
vsite.cpp
legacy
/
include
/
gromacs
/
topology
/
ifunc.h
vsite.cpp
legacy
/
include
/
gromacs
/
mdtypes
/
md_enums.h
vsite.h
legacy
/
include
/
gromacs
/
topology
/
idef.h
vsite.h
legacy
/
include
/
gromacs
/
topology
/
ifunc.h
vsite.h
legacy
/
include
/
gromacs
/
utility
/
real.h
wall.cpp
legacy
/
include
/
gromacs
/
utility
/
arrayref.h
wall.cpp
legacy
/
include
/
gromacs
/
utility
/
basedefinitions.h
wall.cpp
legacy
/
include
/
gromacs
/
utility
/
enumerationhelpers.h
wall.cpp
legacy
/
include
/
gromacs
/
mdtypes
/
md_enums.h
wall.cpp
legacy
/
include
/
gromacs
/
utility
/
smalloc.h
wall.h
legacy
/
include
/
gromacs
/
utility
/
real.h
tests
/
wholemoleculetransform.cpp
legacy
/
include
/
gromacs
/
utility
/
arrayref.h
wholemoleculetransform.cpp
legacy
/
include
/
gromacs
/
utility
/
gmxassert.h
tests
/
wholemoleculetransform.cpp
legacy
/
include
/
gromacs
/
topology
/
idef.h
tests
/
wholemoleculetransform.cpp
legacy
/
include
/
gromacs
/
topology
/
ifunc.h
tests
/
wholemoleculetransform.cpp
legacy
/
include
/
gromacs
/
mdtypes
/
md_enums.h
wholemoleculetransform.h
legacy
/
include
/
gromacs
/
utility
/
arrayref.h
wholemoleculetransform.h
legacy
/
include
/
gromacs
/
utility
/
listoflists.h
Generated on Sat Sep 14 2024 23:13:10 for Gromacs by
1.8.5