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Remove charge group data from t_forcerec
2019-09-19
Ber
k
Hess
Remove charge gro
u
p d
a
ta
from t
_
f
orcer
e
c
commit
|
commitdiff
|
tree
2019-09-19
Berk H
e
ss
Add haveFreeE
n
e
rgyWo
r
k
to
DomainLifetimeWorkload flags
commit
|
commitdiff
|
tree
2019-09-18
B
erk Hess
Added free-energy kernel
p
erformanc
e
note
commit
|
commitdiff
|
tree
2019-09-18
Berk Hess
Fix incorrect DD ndim assertion
commit
|
commitdiff
|
tree
2019-09-17
B
erk H
e
s
s
Remove spuriou
s
newline
f
ro
m
log fil
e
commit
|
commitdiff
|
tree
2019-09-17
Berk Hess
F
ix todos
for u
p
date
g
r
o
ups
commit
|
commitdiff
|
tree
2019-09-16
B
e
rk Hess
Rem
o
v
e
o
bso
l
ete mdp option ns-type
commit
|
commitdiff
|
tree
2019-09-16
Berk Hess
Add virtual si
t
e
type 2FD
commit
|
commitdiff
|
tree
2019-09-16
Berk Hess
Remo
v
e cut-off schemes
f
rom manual
commit
|
commitdiff
|
tree
2019-09-16
Berk Hess
Add opt
i
on request 1
D
DD with 1 pulse
commit
|
commitdiff
|
tree
2019-09-13
Berk
H
ess
Fix nonbon
d
ed-ben
c
h c
o
mpi
l
ation issue
commit
|
commitdiff
|
tree
2019-09-13
B
e
rk Hess
Add nbnxm ker
n
el benchmark tool
commit
|
commitdiff
|
tree
2019-09-12
Berk Hess
Updat
e
d mdp
documen
t
at
i
on for
g
roup sche
m
e removal
commit
|
commitdiff
|
tree
2019-09-12
Berk Hess
Fix master n
o
t co
m
p
i
ling
commit
|
commitdiff
|
tree
2019-09-12
Berk Hess
En
a
ble
TPI
w
ith the Verlet cut-off schem
e
commit
|
commitdiff
|
tree
2019-09-09
Berk Hess
Remo
v
e inc
o
rr
e
c
t check with rf-zero
commit
|
commitdiff
|
tree
2019-09-09
Ber
k
Hess
Extract C
a
rtesian
d
ata f
r
o
m DDRa
n
kSetup
commit
|
commitdiff
|
tree
2019-09-09
Berk
H
e
ss
R
ename DDS
e
tup to DDGr
i
dSetup
commit
|
commitdiff
|
tree
2019-09-09
Berk Hes
s
Clean up PME rank variabl
e
s
commit
|
commitdiff
|
tree
2019-09-09
B
e
r
k Hess
R
efac
t
or init_doma
i
n
_
decomposit
i
on()
commit
|
commitdiff
|
tree
2019-09-06
Berk Hess
Extra
c
t gettin
g
of DDRank
S
e
tup
commit
|
commitdiff
|
tree
2019-09-06
Berk H
e
s
s
Add
P
P
grid
info to DDRankS
e
tup
commit
|
commitdiff
|
tree
2019-09-05
Berk Hess
Extract DDRankSetup from g
m
x_domdec
_
com
m
_t
commit
|
commitdiff
|
tree
2019-09-05
Berk Hess
Sp
l
it off ge
t
t
i
ng of t
h
e D
D
s
etup
commit
|
commitdiff
|
tree
2019-09-04
Berk Hess
Col
l
ect set
t
ings for DD in DDSettin
g
s
commit
|
commitdiff
|
tree
2019-09-04
Berk Hess
Extr
a
c
t
g
etting
of DDSystemInfo
commit
|
commitdiff
|
tree
2019-09-04
Ber
k
H
ess
Si
m
pli
f
y han
d
ling o
f
DD
bonded distances
commit
|
commitdiff
|
tree
2019-09-04
B
erk
Hess
Move
c
onstraint and bonded filt
e
r
ing info into D
D
Sys
t
e
m
Info
commit
|
commitdiff
|
tree
2019-09-04
Berk Hess
M
o
ve update grou
p
ing
to DDS
y
stem
I
nfo
commit
|
commitdiff
|
tree
2019-09-04
Berk Hess
Chang
e
DD pme fo
r
ce buff
e
r
to std::vector
commit
|
commitdiff
|
tree
2019-09-04
Berk Hess
Init
i
aliz
e
all me
m
bers
o
f gmx_
d
omdec_t
commit
|
commitdiff
|
tree
2019-09-03
Be
r
k
Hess
Extract DDSy
s
temInfo from gmx_domdec_comm_t
commit
|
commitdiff
|
tree
2019-09-03
B
erk Hess
Un
i
fy
m
anual
a
n
d
auto
D
D
grid choices
commit
|
commitdiff
|
tree
2019-09-03
Berk Hess
Remove
g
m
x
_domdec_t fr
o
m dd_choose_grid()
commit
|
commitdiff
|
tree
2019-09-03
Berk Hess
Ex
t
a
c
t UnitCellInfo f
r
o
m
g
mx_domdec_t
commit
|
commitdiff
|
tree
2019-09-02
Berk Hess
Only
u
se
fshift wh
e
n needed
commit
|
commitdiff
|
tree
2019-08-22
Berk Hess
F
ix
perturbe
d
bonded
bug
commit
|
commitdiff
|
tree
2019-08-20
Berk Hess
Merge two
d
ihedral functions
commit
|
commitdiff
|
tree
2019-08-20
B
e
rk Hess
Use shiftForce
s
i
n
Force
O
u
pu
t
s
commit
|
commitdiff
|
tree
2019-08-20
Berk He
s
s
Make bonde
d
virial co
m
putation
conditio
n
al
commit
|
commitdiff
|
tree
2019-08-20
B
e
r
k Hess
Fix mi
s
sing bond
e
d forc
e
s with CUDA
GPUs and DD
commit
|
commitdiff
|
tree
2019-08-15
Berk H
e
ss
Te
m
plate bonded interactions on kerne
l
flavor
commit
|
commitdiff
|
tree
2019-08-09
Be
r
k H
e
ss
Move
bonded function table into
bo
n
ded
.
cpp
commit
|
commitdiff
|
tree
2019-08-09
B
e
rk Hess
SIMD
acceleration
fo
r
F_FO
U
RDIHS and F_PIDIHS
commit
|
commitdiff
|
tree
2019-08-06
Berk
He
s
s
A
dd For
c
eWithSh
i
ftForces class
commit
|
commitdiff
|
tree
2019-08-06
Be
r
k
H
e
s
s
Fix latex f
o
rmula in
r
efer
e
nce manua
l
commit
|
commitdiff
|
tree
2019-08-05
Berk
He
s
s
Make box
const i
n
do_f
o
rce()
commit
|
commitdiff
|
tree
2019-08-05
B
e
r
k
H
ess
C
h
ange ForceOutputs to a cla
s
s
commit
|
commitdiff
|
tree
2019-08-03
Berk He
s
s
Remove semicolon from GP
U
T
E
RM mac
r
os
commit
|
commitdiff
|
tree
2019-08-02
Be
r
k
H
e
ss
Made gmx dis
r
e w
o
r
k wit
h
non-c
o
ns
e
cutively labele
d
.
.
.
commit
|
commitdiff
|
tree
2019-08-01
Ber
k
Hess
Remove a pointer
in
t_force
r
ec
commit
|
commitdiff
|
tree
2019-08-01
Berk Hess
Fix nbnxm GPU memory reservati
o
n issue
commit
|
commitdiff
|
tree
2019-07-31
B
e
rk Hess
Re
m
o
v
e unu
s
ed CGLO_INITIALIZATION
commit
|
commitdiff
|
tree
2019-07-31
B
erk
H
ess
Remov
e
vcm
r
emo
v
al from
compute_glo
b
als()
commit
|
commitdiff
|
tree
2019-07-31
Berk Hess
A
d
d g
r
ompp wa
r
ning w
i
th use
o
f GROMOS FF
commit
|
commitdiff
|
tree
2019-07-31
Berk
H
ess
Remove need
for GROMOS FF in
test
commit
|
commitdiff
|
tree
2019-07-30
Berk Hes
s
Use invsq
r
t and cbrt in
free energy kernel
commit
|
commitdiff
|
tree
2019-07-29
Berk Hes
s
R
e
move LJ Ewald cor
r
e
c
tion tables
commit
|
commitdiff
|
tree
2019-07-29
Berk Hess
Add initial
i
zati
o
n
t
o t_nrnb
commit
|
commitdiff
|
tree
2019-07-29
B
e
rk Hess
Fix
s
e
g
mentation f
a
u
lt with cosine pu
l
ling
commit
|
commitdiff
|
tree
2019-07-28
B
er
k
Hess
Removed generalized react
i
on-field
commit
|
commitdiff
|
tree
2019-07-28
Berk Hess
Convert Ewa
l
d correct
i
on tables to C+
+
commit
|
commitdiff
|
tree
2019-07-26
Ber
k
Hess
Add def
a
u
l
t initialization to interaction_const
_
t
commit
|
commitdiff
|
tree
2019-07-26
B
e
r
k Hess
R
em
o
ve
s
h_invr
c
6 from inte
r
a
ctio
n
_const_t
commit
|
commitdiff
|
tree
2019-07-25
Ber
k
Hess
Split canDet
e
c
tGpus()
commit
|
commitdiff
|
tree
2019-07-08
Be
r
k Hess
Store nbnxm gridSet data in Grid
S
etData
commit
|
commitdiff
|
tree
2019-07-05
Berk Hess
Chan
g
e
a
ffinity enum to
e
num class
commit
|
commitdiff
|
tree
2019-07-02
Berk Hess
Refactor thread affinity c
h
ecking
commit
|
commitdiff
|
tree
2019-07-02
Berk
H
ess
Re-e
n
able affinity diagonos
t
i
cs wi
t
h MPI
commit
|
commitdiff
|
tree
2019-07-01
Berk He
s
s
Fix
MPI deadl
o
c
k
i
n aff
i
nity sett
i
n
g
commit
|
commitdiff
|
tree
2019-07-01
Berk Hess
Template
f
ree
-
energy kernel on differing coul/vdw soft
.
.
.
commit
|
commitdiff
|
tree
2019-06-26
B
e
r
k Hes
s
Remo
v
e tabulation fr
o
m
f
ree-energ
y
kernel
commit
|
commitdiff
|
tree
2019-06-20
Berk
Hess
Rem
o
ve unnec
e
ssar
y
#if GM
X
_MPI in pme
c
ode
commit
|
commitdiff
|
tree
2019-06-20
Berk Hess
Template free-
e
nergy ke
r
nel on so
f
t-core
commit
|
commitdiff
|
tree
2019-06-19
Ber
k
Hess
Refacto
r
PME atom handling
commit
|
commitdiff
|
tree
2019-06-19
Berk Hess
Rem
o
ve
d
u
n
used code paths i
n
the NB FE kernel
commit
|
commitdiff
|
tree
2019-06-18
Berk Hes
s
Make forcerec
c
onst i
n
d
i
sp
a
tchNonbondedKernel(
)
commit
|
commitdiff
|
tree
2019-06-17
Be
r
k
Hess
Simplify GPU
nbnxm x c
o
nv
e
rsion
commit
|
commitdiff
|
tree
2019-06-17
B
erk Hes
s
Remove unused nbnxm include fil
e
s
commit
|
commitdiff
|
tree
2019-06-11
Berk Hes
s
Allow AW
H
geomet
r
y
'
di
r
ection'
t
o be periodi
c
commit
|
commitdiff
|
tree
2019-06-10
Berk He
s
s
Fix gmx wham
with ang
l
e
geomet
r
ies
commit
|
commitdiff
|
tree
2019-06-05
B
e
r
k H
e
s
s
Fi
x
refer
e
nce
SIMD memory alignment
commit
|
commitdiff
|
tree
2019-05-29
Berk Hess
Fix mis
s
ing
i
nter
m
olec
u
lar interactions with D
D
commit
|
commitdiff
|
tree
2019-05-27
Be
r
k Hess
Work around gcc 7 avx
5
12
bug
commit
|
commitdiff
|
tree
2019-05-23
Berk Hess
F
i
x SH
A
K
E
dH/dlambda contributi
o
ns
commit
|
commitdiff
|
tree
2019-05-14
Berk
Hess
Make all do_force_l
o
w
level() inp
u
t const
commit
|
commitdiff
|
tree
2019-05-14
Ber
k
Hess
Correct us
e
r
guide postion rest
r
a
int virial
commit
|
commitdiff
|
tree
2019-05-04
Berk H
e
ss
R
e
m
ove PME e
x
c
l
u
s
ion correcti
o
n
commit
|
commitdiff
|
tree
2019-05-03
Berk Hess
Removed non-
e
x
i
stent
A
WH m
d
p
option
commit
|
commitdiff
|
tree
2019-05-03
Berk Hess
Conv
e
rt manage_thr
e
ading_t and gmx_
e
n
erdata_t to C
+
+
commit
|
commitdiff
|
tree
2019-05-02
Be
r
k H
e
ss
C
hange nbnxm FEP pointer to
uniqu
e
_ptr
commit
|
commitdiff
|
tree
2019-04-30
Be
r
k
Hess
A
d
d con/destruct
o
r f
o
r
t_for
c
etable
commit
|
commitdiff
|
tree
2019-04-30
Berk H
e
ss
Convert DispersionCorrection to
a class
commit
|
commitdiff
|
tree
2019-04-18
Berk He
s
s
Remove nbnxm k
e
r
n
e
l type from pairlist generation
commit
|
commitdiff
|
tree
2019-04-18
Berk Hess
R
emove charge
g
r
o
ups
f
ro
m
d
omdec and local
t
op
commit
|
commitdiff
|
tree
2019-04-18
Berk
He
s
s
Fix p
d
b-relate
d
issues
commit
|
commitdiff
|
tree
2019-04-17
Berk
H
ess
Remove group sch
e
me se
a
rch c
o
de
commit
|
commitdiff
|
tree
2019-04-17
Berk He
s
s
S
implify vsite PBC ha
n
dl
i
n
g
commit
|
commitdiff
|
tree
2019-04-17
B
erk
Hess
Reduc
e
n
b
nxm
CPU
k
ernel
a
rguments
commit
|
commitdiff
|
tree
2019-04-17
B
e
rk Hess
Si
m
plify nbnxm shift
force handling
commit
|
commitdiff
|
tree
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