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Fix integration issues
2019-08-22
B
erk Hess
F
ix
p
e
r
turbed bond
e
d b
u
g
commit
|
commitdiff
|
tree
2019-08-20
Berk Hess
Merge two
d
ihe
d
ral
f
u
nctions
commit
|
commitdiff
|
tree
2019-08-20
Berk
Hess
Use shiftFo
r
c
e
s in Forc
e
Oup
u
ts
commit
|
commitdiff
|
tree
2019-08-20
Berk Hess
Mak
e
bonded viria
l
computati
o
n conditional
commit
|
commitdiff
|
tree
2019-08-20
Berk H
e
ss
F
ix missing
bonded forces wi
t
h
CUDA GPUs
and
D
D
commit
|
commitdiff
|
tree
2019-08-15
Berk
Hess
Tem
p
la
t
e bonded interactions on k
e
rne
l
f
l
av
o
r
commit
|
commitdiff
|
tree
2019-08-09
Berk H
e
s
s
M
o
ve
bonded functi
o
n tabl
e
into bonded
.
cpp
commit
|
commitdiff
|
tree
2019-08-09
Berk Hess
SIMD accel
e
r
a
tion
f
or
F
_
F
O
URD
I
HS
a
nd F_PIDIHS
commit
|
commitdiff
|
tree
2019-08-06
Be
r
k Hess
Add Fo
r
ceWithShiftForc
e
s cla
s
s
commit
|
commitdiff
|
tree
2019-08-06
Berk H
e
ss
Fix
l
atex formula in reference m
a
nual
commit
|
commitdiff
|
tree
2019-08-05
B
erk Hess
Ma
k
e b
o
x const
i
n
do_force()
commit
|
commitdiff
|
tree
2019-08-05
Berk Hes
s
C
hange For
c
eOutputs to a class
commit
|
commitdiff
|
tree
2019-08-03
Berk Hess
Remove semicolon from GPU
T
ERM
m
acros
commit
|
commitdiff
|
tree
2019-08-02
Ber
k
H
ess
Made gmx disre
work
wi
t
h non
-
con
s
e
cutively label
e
d
.
.
.
commit
|
commitdiff
|
tree
2019-08-01
Berk Hess
Rem
o
ve a poin
t
e
r
in t
_
f
o
rcerec
commit
|
commitdiff
|
tree
2019-08-01
Be
r
k Hess
F
i
x n
b
nxm GPU mem
o
ry
reservation is
s
ue
commit
|
commitdiff
|
tree
2019-07-31
Be
r
k
H
e
ss
Remove un
u
sed
CGLO_INITIALIZATION
commit
|
commitdiff
|
tree
2019-07-31
Berk He
s
s
R
e
move vcm rem
o
val
f
rom compute_globals()
commit
|
commitdiff
|
tree
2019-07-31
Berk Hess
Add grompp warnin
g
w
i
t
h use of GRO
M
O
S
F
F
commit
|
commitdiff
|
tree
2019-07-31
Berk
H
ess
Remove ne
e
d for GROMO
S
FF
i
n t
e
st
commit
|
commitdiff
|
tree
2019-07-30
Berk
H
ess
Use invsq
r
t
a
nd cbr
t
in free ene
r
g
y kernel
commit
|
commitdiff
|
tree
2019-07-29
Berk Hess
R
e
move LJ Ewald corre
c
ti
o
n tables
commit
|
commitdiff
|
tree
2019-07-29
Berk Hess
Add
i
ni
t
ializatio
n
to t_nrnb
commit
|
commitdiff
|
tree
2019-07-29
Berk Hess
Fix
segm
e
n
tation fault with cosine pu
l
ling
commit
|
commitdiff
|
tree
2019-07-28
Berk Hess
Removed generalized
r
eac
t
ion-field
commit
|
commitdiff
|
tree
2019-07-28
Be
r
k Hess
Convert Ewald correction t
a
bles to C++
commit
|
commitdiff
|
tree
2019-07-26
Berk Hess
Add default
i
nitialization to interacti
o
n_
c
onst_t
commit
|
commitdiff
|
tree
2019-07-26
Berk H
e
ss
Remove s
h
_
i
nvrc6 from interac
t
ion_const_
t
commit
|
commitdiff
|
tree
2019-07-25
Berk
H
ess
Split canDetectGpus()
commit
|
commitdiff
|
tree
2019-07-08
Ber
k
He
s
s
Store nb
n
xm gridSet data in GridSetDa
t
a
commit
|
commitdiff
|
tree
2019-07-05
Berk H
e
ss
Change
affin
i
ty enum to enum cla
s
s
commit
|
commitdiff
|
tree
2019-07-02
Berk Hess
Ref
a
ctor thre
a
d affi
n
ity
c
he
c
kin
g
commit
|
commitdiff
|
tree
2019-07-02
Berk He
s
s
Re-e
n
a
b
l
e
affinity diagonostics wit
h
MPI
commit
|
commitdiff
|
tree
2019-07-01
Berk
Hess
F
i
x
MPI dead
l
ock
in
affinity se
t
ting
commit
|
commitdiff
|
tree
2019-07-01
Berk Hess
Templa
t
e free-energy kernel on
diffe
r
ing coul/v
d
w sof
t
.
.
.
commit
|
commitdiff
|
tree
2019-06-26
Berk Hess
Remov
e
tabul
a
t
ion from f
r
ee-ene
r
gy ke
r
n
e
l
commit
|
commitdiff
|
tree
2019-06-20
B
e
r
k
Hess
Remove
unnecessary #
i
f GMX_MPI in pme
c
ode
commit
|
commitdiff
|
tree
2019-06-20
Berk Hes
s
T
emplat
e
f
ree
-
energy kernel o
n
soft-c
o
re
commit
|
commitdiff
|
tree
2019-06-19
Berk Hess
Refactor PME atom handl
i
n
g
commit
|
commitdiff
|
tree
2019-06-19
B
e
rk Hes
s
R
e
m
ov
e
d
u
nused code paths in the
N
B F
E
kernel
commit
|
commitdiff
|
tree
2019-06-18
Berk
Hess
Make
f
orcerec const
i
n dispatchNonbondedKern
e
l()
commit
|
commitdiff
|
tree
2019-06-17
Berk Hess
Simplify GPU
nb
n
xm x conversion
commit
|
commitdiff
|
tree
2019-06-17
Berk He
s
s
Remove unu
s
ed nbnxm inclu
d
e fil
e
s
commit
|
commitdiff
|
tree
2019-06-11
Berk H
e
s
s
Allow A
W
H geometry
'd
i
recti
o
n' to b
e
p
e
riodic
commit
|
commitdiff
|
tree
2019-06-10
B
e
rk Hess
Fix
g
mx wha
m
with
angle geometr
i
es
commit
|
commitdiff
|
tree
2019-06-05
Berk
Hess
F
i
x refer
e
nce SIMD memory alignm
e
nt
commit
|
commitdiff
|
tree
2019-05-29
B
e
rk Hess
F
i
x mis
s
ing in
t
e
r
molecular interaction
s
with
DD
commit
|
commitdiff
|
tree
2019-05-27
Be
r
k
H
ess
Wo
r
k arou
n
d
gcc 7 avx512 bug
commit
|
commitdiff
|
tree
2019-05-23
Berk Hess
Fix SHAKE dH/dlambda
contributions
commit
|
commitdiff
|
tree
2019-05-14
Be
r
k H
e
ss
Make all do_force_lowlevel() input
co
n
st
commit
|
commitdiff
|
tree
2019-05-14
Berk Hess
Correct u
s
er guide postion restraint
v
irial
commit
|
commitdiff
|
tree
2019-05-04
B
e
rk Hess
Remov
e
PME exclu
s
ion c
o
rr
e
ction
commit
|
commitdiff
|
tree
2019-05-03
Berk Hess
Removed non
-
e
x
i
s
tent
A
WH mdp option
commit
|
commitdiff
|
tree
2019-05-03
Berk Hess
Conve
r
t manage_threading_t and gmx_enerdata_t
t
o
C++
commit
|
commitdiff
|
tree
2019-05-02
Berk He
s
s
Ch
a
nge nbn
x
m FEP pointer to unique
_
pt
r
commit
|
commitdiff
|
tree
2019-04-30
B
erk Hess
Add con/
d
estructor for
t
_
forcetable
commit
|
commitdiff
|
tree
2019-04-30
Berk Hess
Conver
t
Dispers
i
onCorrection
t
o a class
commit
|
commitdiff
|
tree
2019-04-18
Berk Hess
Remove nbnxm ke
r
n
el type from pa
i
rlist gen
e
ration
commit
|
commitdiff
|
tree
2019-04-18
Ber
k
He
s
s
Remove ch
a
r
ge gro
u
p
s from domdec and localtop
commit
|
commitdiff
|
tree
2019-04-18
B
e
rk Hess
Fix pdb
-
rela
t
ed
i
s
s
u
es
commit
|
commitdiff
|
tree
2019-04-17
Berk Hess
Remove group sche
m
e search code
commit
|
commitdiff
|
tree
2019-04-17
B
e
rk Hes
s
Simplify vsite PBC
ha
n
dling
commit
|
commitdiff
|
tree
2019-04-17
Berk Hess
Reduce nbnxm CPU ker
n
el arguments
commit
|
commitdiff
|
tree
2019-04-17
Berk Hess
S
i
mplify nbnxm shi
f
t fo
r
ce ha
n
dlin
g
commit
|
commitdiff
|
tree
2019-04-16
B
e
rk Hess
S
i
m
plify nb
n
xm buffer
c
learing
commit
|
commitdiff
|
tree
2019-04-16
Ber
k
Hess
Remove RF_excl
_
correction(
)
commit
|
commitdiff
|
tree
2019-04-16
Be
r
k Hess
Ma
k
e mdr
u
n -
n
ste
p
s wor
k
aga
i
n
.
commit
|
commitdiff
|
tree
2019-04-15
B
er
k
Hess
Updat
e
2019
release note
s
for i
s
sue 2845
commit
|
commitdiff
|
tree
2019-04-15
Berk Hess
Fix pdb-related issues
commit
|
commitdiff
|
tree
2019-04-15
B
e
rk
H
ess
Disallow pull geome
t
ry dire
c
tion-periodi
c
with AWH
commit
|
commitdiff
|
tree
2019-03-28
Berk Hess
S
implify nbnxm final
f
orce
r
e
duction
commit
|
commitdiff
|
tree
2019-03-28
Berk
Hess
Move early r
e
tur
n
fo
r
nbnxm
f
or
c
e red
u
ct
i
on
commit
|
commitdiff
|
tree
2019-03-28
Berk
H
ess
M
ove
PairlistSet
d
e
claration
commit
|
commitdiff
|
tree
2019-03-28
B
e
rk Hess
Move
n
bnxm domai
n
Setup to
GridSet
commit
|
commitdiff
|
tree
2019-03-28
Berk Hes
s
Extra
c
t nbnx
m
Pairl
i
s
tSets
commit
|
commitdiff
|
tree
2019-03-27
Berk Hes
s
Fix nbnxm OpenCL with
cl
u
ster size 4
commit
|
commitdiff
|
tree
2019-03-25
Berk Hess
Convert nbnxn_pairl
i
s
t
_set_t to cl
a
ss Pa
i
rl
i
s
tSet
commit
|
commitdiff
|
tree
2019-03-20
Berk Hess
Move around PairSearch co
d
e
commit
|
commitdiff
|
tree
2019-03-19
Berk Hess
Reduc
e
depen
d
enc
i
es of nbnxn_atomdata
_
t
commit
|
commitdiff
|
tree
2019-03-15
B
er
k
Hes
s
Change nbnxn_search to
cla
s
s Pair
S
earch
commit
|
commitdiff
|
tree
2019-03-15
Ber
k
Hess
Extrac
t
D
oma
i
nSetup from nb
n
xn_search
commit
|
commitdiff
|
tree
2019-03-14
Berk Hess
Chan
g
e
n
b
n
xm macr
o
s to c
o
n
st
e
xpr
commit
|
commitdiff
|
tree
2019-03-14
Berk
H
e
ss
Move functions to g
r
idset
.
c
pp
commit
|
commitdiff
|
tree
2019-03-14
Be
r
k Hess
Add nbnxm G
r
idSet cla
s
s
commit
|
commitdiff
|
tree
2019-03-14
Berk Hess
Fix comp
i
lation issue
commit
|
commitdiff
|
tree
2019-03-12
Berk H
e
ss
Move
nb
n
x
m
atom
m
a
cros t
o
a
t
o
mdata
.
h
commit
|
commitdiff
|
tree
2019-03-11
B
e
rk
H
ess
Add
grompp wa
r
n
ing with use of GROMOS FF
commit
|
commitdiff
|
tree
2019-03-08
Be
r
k Hess
Clea
n
up calc_
v
er
l
e
t
_
b
uffer_siz
e
(
)
commit
|
commitdiff
|
tree
2019-03-06
B
erk Hess
Clea
n
up nbnxm bou
n
d
i
ng box
functions
commit
|
commitdiff
|
tree
2019-03-06
B
e
r
k Hess
Clean
u
p nbnx
m
bound
i
n
g
boxes
commit
|
commitdiff
|
tree
2019-03-06
Berk Hess
Co
n
ve
r
t
nbnxm bo
u
nding box to a struct
commit
|
commitdiff
|
tree
2019-03-05
Ber
k
Hes
s
Fix post-s
u
bmit war
n
ings
commit
|
commitdiff
|
tree
2019-03-05
Berk He
s
s
Move
nbnx
m
atomdata types to
at
o
mdata
.
h
commit
|
commitdiff
|
tree
2019-03-05
Berk Hess
Turn nbnxn_grid_t into a class
commit
|
commitdiff
|
tree
2019-02-28
B
e
rk Hess
Use un
i
que_ptr in nonbonded_verlet_
t
commit
|
commitdiff
|
tree
2019-02-27
Berk Hess
Use new/delete
for t_forc
e
r
ec
commit
|
commitdiff
|
tree
2019-02-27
Berk He
s
s
Clean up dispersionco
r
rection
.
cpp
commit
|
commitdiff
|
tree
2019-02-27
Berk Hess
Fix 4 comp
i
lers warnings
commit
|
commitdiff
|
tree
2019-02-27
Berk Hes
s
Collect d
i
spersion corr
e
ction code
commit
|
commitdiff
|
tree
2019-02-26
Berk Hess
Correct gro
m
pp
index file error messa
g
e
commit
|
commitdiff
|
tree
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