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Python wrapping code for gmxapi mdrun bindings.
2019-09-02
Berk Hess
Only use fshif
t
when needed
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commitdiff
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tree
2019-08-22
Berk H
e
ss
F
ix perturbed bonded bu
g
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commitdiff
|
tree
2019-08-20
Berk Hes
s
Merg
e
two dihed
r
al functions
commit
|
commitdiff
|
tree
2019-08-20
Berk Hess
Use shiftForces
in Force
O
u
p
u
t
s
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commitdiff
|
tree
2019-08-20
Berk H
e
ss
Make bonded virial computation c
o
n
ditional
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|
commitdiff
|
tree
2019-08-20
Berk Hess
Fix mi
s
sing bonded
forces w
i
t
h CUDA GPUs an
d
D
D
commit
|
commitdiff
|
tree
2019-08-15
B
e
r
k Hess
Template bon
d
e
d i
n
teractions on kernel f
l
avor
commit
|
commitdiff
|
tree
2019-08-09
Ber
k
Hess
M
o
v
e
b
o
nded funct
i
on table into b
o
nded
.
cpp
commit
|
commitdiff
|
tree
2019-08-09
B
e
r
k
Hess
S
IMD accel
e
ration for F_
F
OURDIHS and
F_PIDIHS
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|
commitdiff
|
tree
2019-08-06
Berk H
e
ss
Add Force
W
it
h
S
h
iftForces class
commit
|
commitdiff
|
tree
2019-08-06
Berk Hess
Fix
l
at
e
x
f
o
r
m
u
la in refer
e
n
ce manual
commit
|
commitdiff
|
tree
2019-08-05
B
e
rk Hess
Make box const in do_for
c
e()
commit
|
commitdiff
|
tree
2019-08-05
Berk
H
ess
C
hange
For
c
eOutputs to
a c
l
ass
commit
|
commitdiff
|
tree
2019-08-03
B
e
r
k Hess
Remo
v
e
se
m
icolon
from
G
PU TERM
macros
commit
|
commitdiff
|
tree
2019-08-02
Berk
H
e
s
s
Made gm
x
disre work with non-con
s
ecut
i
v
ely l
a
beled
.
.
.
commit
|
commitdiff
|
tree
2019-08-01
Berk Hess
Remove a pointe
r
in t_f
o
rcerec
commit
|
commitdiff
|
tree
2019-08-01
Be
r
k Hess
Fix
n
b
nxm GPU m
e
mory
reser
v
ati
o
n
is
s
ue
commit
|
commitdiff
|
tree
2019-07-31
Berk Hess
Rem
o
v
e
u
nused CGLO_
I
NITIALIZATION
commit
|
commitdiff
|
tree
2019-07-31
B
erk Hess
Remo
v
e vcm
r
e
m
o
val from compute_g
l
obals()
commit
|
commitdiff
|
tree
2019-07-31
Be
r
k Hess
A
d
d grompp warn
i
ng with use
o
f GR
O
MOS
FF
commit
|
commitdiff
|
tree
2019-07-31
Berk Hess
Remov
e
nee
d
for GROMOS F
F
i
n
test
commit
|
commitdiff
|
tree
2019-07-30
Ber
k
Hess
Use invsqrt an
d
cbrt in
f
r
e
e energy kern
e
l
commit
|
commitdiff
|
tree
2019-07-29
Ber
k
Hess
Remove LJ Ewald co
r
r
ection table
s
commit
|
commitdiff
|
tree
2019-07-29
Berk Hess
Ad
d
initializa
t
ion to
t
_nr
n
b
commit
|
commitdiff
|
tree
2019-07-29
Ber
k
Hess
Fix segmentation fault with cosine pull
i
ng
commit
|
commitdiff
|
tree
2019-07-28
Berk Hes
s
Re
m
o
v
ed genera
l
i
zed reaction-fie
l
d
commit
|
commitdiff
|
tree
2019-07-28
B
e
rk H
e
ss
Conver
t
Ewald
c
orrection table
s
to C++
commit
|
commitdiff
|
tree
2019-07-26
Ber
k
Hess
Add
d
e
fault
i
nitia
l
ization to inter
a
ction_c
o
nst_t
commit
|
commitdiff
|
tree
2019-07-26
B
erk Hess
Remov
e
sh_inv
r
c6 from int
e
rac
t
ion_const_
t
commit
|
commitdiff
|
tree
2019-07-25
B
e
rk Hess
S
p
lit
c
a
nDet
e
c
tGpus()
commit
|
commitdiff
|
tree
2019-07-08
B
e
rk He
s
s
S
tore nb
n
xm gridSet d
a
ta i
n
Gr
i
dSetData
commit
|
commitdiff
|
tree
2019-07-05
Berk Hess
Change
a
ffinity enum to enu
m
class
commit
|
commitdiff
|
tree
2019-07-02
Ber
k
H
e
ss
Refactor
thread affinity
c
hecking
commit
|
commitdiff
|
tree
2019-07-02
Berk He
s
s
Re-enable affi
n
i
t
y
dia
g
onostics with MPI
commit
|
commitdiff
|
tree
2019-07-01
Berk Hess
Fix M
P
I dea
d
lock in affinity setting
commit
|
commitdiff
|
tree
2019-07-01
Berk H
e
ss
T
e
mp
l
ate free-energy
k
ernel on differin
g
coul/vdw soft
.
.
.
commit
|
commitdiff
|
tree
2019-06-26
Berk
Hess
Remove t
a
bu
l
ation
f
r
om
f
ree-energy kernel
commit
|
commitdiff
|
tree
2019-06-20
B
e
rk Hess
R
emov
e
unnecessary #if GM
X
_MPI in pme code
commit
|
commitdiff
|
tree
2019-06-20
Berk Hess
Tem
p
late fre
e
-energy
k
ernel on so
f
t-core
commit
|
commitdiff
|
tree
2019-06-19
B
erk Hess
Re
f
act
o
r PME atom handling
commit
|
commitdiff
|
tree
2019-06-19
B
erk
Hess
Removed u
n
us
e
d
c
ode pat
h
s in the NB FE kernel
commit
|
commitdiff
|
tree
2019-06-18
Berk Hes
s
Make forcere
c
const in
dispatchNonbondedKernel()
commit
|
commitdiff
|
tree
2019-06-17
Berk Hess
S
implify GPU nbnxm x conversion
commit
|
commitdiff
|
tree
2019-06-17
Berk Hes
s
Remove unused nb
n
xm inc
l
u
de
f
iles
commit
|
commitdiff
|
tree
2019-06-11
Berk Hess
Allow AWH geome
t
ry 'direction' to be periodic
commit
|
commitdiff
|
tree
2019-06-10
Berk Hess
Fix gmx wham with
a
ngl
e
geometries
commit
|
commitdiff
|
tree
2019-06-05
Berk Hess
Fix reference SIMD
m
e
m
ory alignment
commit
|
commitdiff
|
tree
2019-05-29
Berk He
s
s
Fix missing
i
n
t
ermolecular interactions with
DD
commit
|
commitdiff
|
tree
2019-05-27
Berk
Hess
Work around gcc 7 avx
5
12 bug
commit
|
commitdiff
|
tree
2019-05-23
Berk Hess
F
i
x SHAKE
d
H/dl
a
mbd
a
contri
b
utions
commit
|
commitdiff
|
tree
2019-05-14
Berk Hess
M
ake all do_force
_
lowlevel() input con
s
t
commit
|
commitdiff
|
tree
2019-05-14
Berk Hess
Correct
u
s
e
r guide postion res
t
rai
n
t vi
r
ial
commit
|
commitdiff
|
tree
2019-05-04
B
e
rk Hess
Remove PME exclusion correction
commit
|
commitdiff
|
tree
2019-05-03
B
er
k
Hess
Remove
d
n
on-existent AWH mdp
o
ption
commit
|
commitdiff
|
tree
2019-05-03
Berk Hes
s
Conv
e
rt manage_threadin
g
_t and g
m
x
_
e
n
er
d
ata_t to C++
commit
|
commitdiff
|
tree
2019-05-02
Berk Hess
Change n
b
nxm FEP
p
oint
e
r to
unique_ptr
commit
|
commitdiff
|
tree
2019-04-30
Berk Hess
A
d
d con/destruc
t
or
f
o
r t
_
fo
r
c
e
tab
l
e
commit
|
commitdiff
|
tree
2019-04-30
Berk
H
ess
Convert DispersionCorrection to a class
commit
|
commitdiff
|
tree
2019-04-18
Berk Hess
R
e
move
nbnxm
kernel type from pai
r
list g
e
neration
commit
|
commitdiff
|
tree
2019-04-18
Berk
H
e
ss
Remove char
g
e
g
r
o
u
p
s
from domdec and l
o
cal
t
o
p
commit
|
commitdiff
|
tree
2019-04-18
B
e
rk
H
ess
F
ix pdb-re
l
a
t
ed
i
ssues
commit
|
commitdiff
|
tree
2019-04-17
B
e
rk Hess
R
e
mo
v
e group
scheme search
code
commit
|
commitdiff
|
tree
2019-04-17
B
erk H
e
s
s
Si
m
p
l
ify
v
site PBC h
a
ndling
commit
|
commitdiff
|
tree
2019-04-17
Berk Hess
R
e
duce nbnxm CPU kernel a
r
guments
commit
|
commitdiff
|
tree
2019-04-17
Berk
Hess
Simpli
f
y nbnxm shift force handling
commit
|
commitdiff
|
tree
2019-04-16
Berk Hess
Simplify nbnxm
b
uf
f
er cleari
n
g
commit
|
commitdiff
|
tree
2019-04-16
Ber
k
H
ess
Remov
e
RF
_
e
xcl_correction()
commit
|
commitdiff
|
tree
2019-04-16
Berk
H
ess
Make mdrun -nsteps
w
ork
a
gain
.
commit
|
commitdiff
|
tree
2019-04-15
Berk Hess
Update 2019 release
n
otes for issue 2845
commit
|
commitdiff
|
tree
2019-04-15
Berk H
e
ss
Fix pdb-related issues
commit
|
commitdiff
|
tree
2019-04-15
Berk Hess
D
isallo
w
pull geometry di
r
ecti
o
n-periodic with A
W
H
commit
|
commitdiff
|
tree
2019-03-28
Berk Hess
Simplify nbn
x
m final force reduction
commit
|
commitdiff
|
tree
2019-03-28
Ber
k
H
ess
Mo
v
e early r
e
turn fo
r
nbnxm f
o
rce re
d
uction
commit
|
commitdiff
|
tree
2019-03-28
B
e
rk
H
ess
Move PairlistS
e
t
de
c
larat
i
on
commit
|
commitdiff
|
tree
2019-03-28
Be
r
k He
s
s
Move nbnxm doma
i
nSetup to GridSet
commit
|
commitdiff
|
tree
2019-03-28
Berk Hess
Extract nb
n
xm Pai
r
listSets
commit
|
commitdiff
|
tree
2019-03-27
B
e
rk Hess
F
ix nbnx
m
OpenCL with
cluster
s
ize 4
commit
|
commitdiff
|
tree
2019-03-25
Berk Hess
Conver
t
nbnxn_
p
airli
s
t_set_t to class Pairl
i
stSet
commit
|
commitdiff
|
tree
2019-03-20
Berk Hess
Move
around PairSearc
h
c
ode
commit
|
commitdiff
|
tree
2019-03-19
Berk H
e
ss
R
e
duce
d
ependencies of n
b
nxn_atomdat
a
_t
commit
|
commitdiff
|
tree
2019-03-15
B
e
r
k Hess
Change nb
n
x
n_search to class PairSe
a
rch
commit
|
commitdiff
|
tree
2019-03-15
Berk
H
e
s
s
Ext
r
act Dom
a
inSetup from nbnxn_search
commit
|
commitdiff
|
tree
2019-03-14
Berk He
s
s
Cha
n
ge nbnxm macros to constexpr
commit
|
commitdiff
|
tree
2019-03-14
Berk
Hess
M
o
ve functions to g
r
idse
t
.
cpp
commit
|
commitdiff
|
tree
2019-03-14
Berk
Hess
Add nbnxm GridSet cl
a
ss
commit
|
commitdiff
|
tree
2019-03-14
Berk Hess
Fix compilation issue
commit
|
commitdiff
|
tree
2019-03-12
B
e
rk H
e
ss
Move nbnxm atom m
a
cros to at
o
mdata
.
h
commit
|
commitdiff
|
tree
2019-03-11
Berk Hess
Add
g
rompp warning with use of GROMOS FF
commit
|
commitdiff
|
tree
2019-03-08
Berk Hess
Clea
n
up calc_verlet_
b
uffer_size()
commit
|
commitdiff
|
tree
2019-03-06
Berk Hess
Cl
e
a
n
up nbnxm bound
i
ng box f
u
nctions
commit
|
commitdiff
|
tree
2019-03-06
Berk Hess
Clean up nbn
x
m boundi
n
g
b
oxes
commit
|
commitdiff
|
tree
2019-03-06
Berk Hess
Con
v
ert nbnx
m
bo
u
n
d
in
g
bo
x
to
a struc
t
commit
|
commitdiff
|
tree
2019-03-05
B
e
rk Hess
Fix p
o
s
t
-submit warnings
commit
|
commitdiff
|
tree
2019-03-05
Ber
k
Hess
Move
n
bnxm at
o
mdata types to atomdat
a
.
h
commit
|
commitdiff
|
tree
2019-03-05
Berk Hess
Turn nbnxn
_
grid_t into a class
commit
|
commitdiff
|
tree
2019-02-28
Ber
k
Hess
U
se
unique
_
pt
r
in nonbond
e
d_v
e
rlet_t
commit
|
commitdiff
|
tree
2019-02-27
Ber
k
Hess
Use
new/delete for t_forcer
e
c
commit
|
commitdiff
|
tree
2019-02-27
Berk
He
s
s
Clean up d
i
spersioncorrecti
o
n
.
cpp
commit
|
commitdiff
|
tree
2019-02-27
Berk Hess
Fix 4 comp
i
lers wa
r
ni
n
gs
commit
|
commitdiff
|
tree
2019-02-27
Berk Hess
Coll
e
ct dispersion
c
orrectio
n
code
commit
|
commitdiff
|
tree
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