repo.or.cz
/
gromacs.git
/
search
commit
grep
author
committer
pickaxe
?
search:
re
summary
|
log
|
graphiclog1
|
graphiclog2
|
commit
|
commitdiff
|
tree
|
refs
|
edit
|
fork
first
·
prev
·
next
Make Cygwin build work
2020-05-20
Berk Hess
Remove t_m
d
atoms from
N
bnxm
setAtomPr
o
p
e
rties()
commit
|
commitdiff
|
tree
2020-05-19
B
e
rk Hes
s
Ref
a
ctor
p
rin
t
_m
i
ssing_interac
t
ion
s
()
commit
|
commitdiff
|
tree
2020-05-14
Berk He
s
s
Extract
postProcessForceWithShiftForces()
commit
|
commitdiff
|
tree
2020-05-12
Berk Hess
Extra
c
t helper force buffe
r
s to a separa
t
e cl
a
ss
commit
|
commitdiff
|
tree
2020-05-12
B
e
rk He
s
s
R
efactor virtual site interface
commit
|
commitdiff
|
tree
2020-04-06
B
e
r
k Hess
Move force buffer resizing to mdsetup
commit
|
commitdiff
|
tree
2020-03-20
Ber
k
Hess
Rename c
l
ass Grid to BiasGr
i
d
i
n AWH module
commit
|
commitdiff
|
tree
2020-03-19
Be
r
k He
s
s
Sim
p
lify fi
n
is
h
_update()
commit
|
commitdiff
|
tree
2020-03-19
Berk
Hess
Remove at_sta
r
t
f
rom
t_graph
commit
|
commitdiff
|
tree
2020-03-18
Berk Hess
Remove use of g
r
aph i
n
do_forc
e
(
)
commit
|
commitdiff
|
tree
2020-03-18
B
e
rk H
e
ss
Use Who
l
eMoleculeT
r
ansform fo
r
o
r
i
res and epsilon-surface
commit
|
commitdiff
|
tree
2020-03-18
Berk
H
ess
Add Wh
o
leM
o
l
ec
u
leTr
a
nsform class
commit
|
commitdiff
|
tree
2020-03-17
Berk
Hes
s
Convert
t
_graph to C++
commit
|
commitdiff
|
tree
2020-03-17
Ber
k
H
ess
Dis
a
b
l
e Ewald
dipole corre
c
tion
wit
h
out DD
commit
|
commitdiff
|
tree
2020-03-13
Ber
k
Hess
Add tests for
Ewald surfa
c
e t
e
rms
commit
|
commitdiff
|
tree
2020-03-11
Berk H
e
s
s
Add tests for
gra
p
h
commit
|
commitdiff
|
tree
2020-03-10
Berk He
s
s
Fix type in
ra
n
ge and add t
e
sts
commit
|
commitdiff
|
tree
2020-03-07
B
e
rk Hess
Make shake work without g
r
a
ph
commit
|
commitdiff
|
tree
2020-03-05
Be
r
k Hess
Add
I
nteractionDefi
n
itions
commit
|
commitdiff
|
tree
2020-03-02
Berk Hess
Fix center of
m
ass motion removal wi
t
h frozen atoms
commit
|
commitdiff
|
tree
2020-03-02
Be
r
k
Hess
F
i
x grompp unbound atom
c
heck
commit
|
commitdiff
|
tree
2020-03-02
Berk He
s
s
Fi
x
nrdf
with partial COMM re
m
oval
commit
|
commitdiff
|
tree
2020-03-02
Ber
k
Hess
Fix too small
pairlist b
u
f
fer on Intel GPUs
commit
|
commitdiff
|
tree
2020-02-21
Berk Hess
Add fatal erro
r
wh
e
n
multisim ru
n
s shar
i
ng state have
.
.
.
commit
|
commitdiff
|
tree
2020-02-15
Berk Hess
R
e
mov
e
1 pulse DD
request
commit
|
commitdiff
|
tree
2020-02-05
B
e
rk Hess
A
ctu
a
l
ly fix PM
E
f
o
rces with FE w
i
th
o
ut perturbed q/LJ
commit
|
commitdiff
|
tree
2020-02-04
Berk Hes
s
Actua
l
l
y
fix
P
ME fo
r
c
es with FE without perturbed q/LJ
commit
|
commitdiff
|
tree
2020-01-23
B
erk Hess
Fix
D
D rank c
o
unt prime ch
e
ck
commit
|
commitdiff
|
tree
2020-01-22
B
e
rk Hess
M
i
no
r
cleanup i
n
constraint and shellfc code
commit
|
commitdiff
|
tree
2020-01-22
Berk Hess
F
i
x
illegal memo
r
y acces
s
i
n PME commun
i
cation
commit
|
commitdiff
|
tree
2020-01-22
Berk Hess
C
larify COMM/posres grompp
n
o
te
commit
|
commitdiff
|
tree
2020-01-20
Berk Hess
Use Array
R
ef(
W
i
thPadding) in c
o
ns
t
rai
n
t code
commit
|
commitdiff
|
tree
2020-01-20
Be
r
k Hess
U
se std::
v
ector in shellfc
commit
|
commitdiff
|
tree
2020-01-17
Berk
H
ess
Add check for
s
hells an
d
G
PU update
commit
|
commitdiff
|
tree
2020-01-16
Ber
k
Hess
Correct fixed
redmine
issue i
d
f
rom 3297
t
o 3296
commit
|
commitdiff
|
tree
2020-01-15
Berk H
e
ss
Fix mu
l
t
i
sim
w
ith parallel simulati
o
n
commit
|
commitdiff
|
tree
2020-01-13
Ber
k
Hes
s
Avoid unnecessary exc
l
usion g
e
nerati
o
n in DD
commit
|
commitdiff
|
tree
2019-12-22
B
erk Hes
s
U
s
e
L
istOfLists fo
r
atom
to
c
onst
r
aint mapping
commit
|
commitdiff
|
tree
2019-12-22
Be
r
k Hess
Move nr_nonpe
r
tu
r
bed
o
ut of t_i
l
ist
commit
|
commitdiff
|
tree
2019-12-19
Berk Hess
E
x
p
a
nd ListOfLi
s
ts pushBack() functi
o
nality
commit
|
commitdiff
|
tree
2019-12-19
B
e
rk Hes
s
Remove exc
l
usions from t
_
topol
o
gy
commit
|
commitdiff
|
tree
2019-12-19
Berk Hess
Fix mdrun appe
n
d
i
ng
i
n
v
a
lidating energy files
commit
|
commitdiff
|
tree
2019-12-18
Berk Hess
C
hange
g
rompp de
c
oupling SD warning
to no
t
e
commit
|
commitdiff
|
tree
2019-12-17
Ber
k
Hess
Add note
f
or C
O
M r
e
moval
w
i
th position r
e
s
t
raints
commit
|
commitdiff
|
tree
2019-12-16
Be
r
k Hess
Us
e
ListOfList
s
in gmx_mtop_t an
d
gmx_localto
p
_
t
commit
|
commitdiff
|
tree
2019-12-16
Berk Hess
F
ix issue
s
in
L
is
t
OfLi
s
ts
commit
|
commitdiff
|
tree
2019-12-12
Berk Hess
Add cla
s
s
L
ist
O
fLists
commit
|
commitdiff
|
tree
2019-12-02
Berk Hes
s
Add
c
h
eck for
coupled c
o
nst
r
aints for CUDA up
d
ate
commit
|
commitdiff
|
tree
2019-12-02
B
e
rk H
e
ss
Extract LI
N
CS CUDA
helper functions
commit
|
commitdiff
|
tree
2019-11-29
Berk He
s
s
Me
r
ge "Merge branch
r
elease-2019 in
t
o
release-2020
.
.
.
commit
|
commitdiff
|
tree
2019-11-28
Berk
Hess
Update documena
t
i
o
n fo
r
NPT GPU up
d
ate
commit
|
commitdiff
|
tree
2019-11-28
Berk Hess
Rem
o
ve assertion
f
ailure in AWH without
i
n
i
t
i
al stage
commit
|
commitdiff
|
tree
2019-11-28
Berk Hess
F
i
x
bug
with G
P
U pressure scaling at non T-sc
a
li
n
g
.
.
.
commit
|
commitdiff
|
tree
2019-11-26
B
e
rk Hess
Fix issues with AWH with p
e
riodic pulling
commit
|
commitdiff
|
tree
2019-11-20
Berk Hess
Quiet pdb2gmx and use gmx_fata
l
commit
|
commitdiff
|
tree
2019-11-19
Berk
H
e
ss
Fix bon
d
ed
atom
c
om
m
unication perf
o
rmance
commit
|
commitdiff
|
tree
2019-11-18
Berk Hess
F
i
x
i
ntermolecula
r
interactions with DD
commit
|
commitdiff
|
tree
2019-11-14
Berk Hess
Simplify t_
f
orcerec
d
est
r
uction
commit
|
commitdiff
|
tree
2019-11-07
Berk Hess
Fix
.
gr
o
large box
wr
i
ting
commit
|
commitdiff
|
tree
2019-11-06
B
er
k
Hess
Depr
e
cated sc-r-power
=
48
commit
|
commitdiff
|
tree
2019-11-01
Berk
H
e
ss
Add ha
v
eE
w
aldSurfaceContri
b
ution to
S
imulation
W
or
k
lo
a
d
commit
|
commitdiff
|
tree
2019-10-31
Berk
H
e
s
s
Update G
P
U updat
e
restrictions
commit
|
commitdiff
|
tree
2019-10-30
Berk
Hess
Fix
w
alls with GPU upd
a
te
commit
|
commitdiff
|
tree
2019-10-29
Berk
Hess
Add mdrun GPU
up
d
a
te docume
n
t
a
tion
commit
|
commitdiff
|
tree
2019-10-29
Ber
k
Hess
F
ix Ewald dipole correction wi
t
h GPU updat
e
commit
|
commitdiff
|
tree
2019-10-29
Berk Hes
s
Di
s
able pressure coupl
i
ng with GPU
updat
e
commit
|
commitdiff
|
tree
2019-10-24
Berk Hess
A
d
d bool u
s
e
DomainDec
o
mp
o
sition i
n
mdrunner
commit
|
commitdiff
|
tree
2019-10-24
Berk Hess
Add g
m
x_mtop_i
n
terac
t
i
o
n
_c
o
u
n
t()
commit
|
commitdiff
|
tree
2019-10-24
Berk Hes
s
Fix initializers in local
i
ty
.
h
commit
|
commitdiff
|
tree
2019-10-23
Be
r
k Hess
Move locality
.
h from nbnxm to
mdtypes
commit
|
commitdiff
|
tree
2019-10-23
Ber
k
H
e
ss
Use gmx::Range in Nbnxm gridding funct
i
ons
commit
|
commitdiff
|
tree
2019-10-23
Ber
k
Hess
Fix illegal me
m
or
y
a
c
cess in FE
calcul
a
tions
commit
|
commitdiff
|
tree
2019-10-23
B
e
rk Hess
E
x
pa
n
d documentation
for nbnxn_p
u
t
_on
_
grid()
commit
|
commitdiff
|
tree
2019-10-22
Berk
Hess
Requi
r
e -ei for e
s
sential dynam
i
c
s
commit
|
commitdiff
|
tree
2019-10-18
Berk H
e
ss
Update grompp cutoff-sch
e
me warn
i
ngs
commit
|
commitdiff
|
tree
2019-10-15
Berk Hess
C
o
ns
t
c
orrectne
s
s for
g
en
h
ydro
commit
|
commitdiff
|
tree
2019-10-12
Berk
Hess
Ad
d
c
lass FixedCapacityVector
commit
|
commitdiff
|
tree
2019-10-09
Ber
k
H
ess
I
n
crease sp
c
min
i
miz
a
tion
test tol
e
rance
commit
|
commitdiff
|
tree
2019-10-09
Berk Hess
Fix h
a
rml
e
ss OpenMP
w
ri
t
e race
commit
|
commitdiff
|
tree
2019-10-09
Berk H
e
ss
Fix G
P
U atom data init
t
im
e
r issue
commit
|
commitdiff
|
tree
2019-10-09
Berk
H
ess
Fix rando
m
en
e
rgy and virial with PME on G
P
U o
n
a
P
ME
.
.
.
commit
|
commitdiff
|
tree
2019-10-08
Berk He
s
s
Make nbnxm a
pro
p
er module
commit
|
commitdiff
|
tree
2019-10-08
Berk Hess
S
i
m
p
lify
ewald
_
LRco
r
re
c
t
ion() call s
i
gnature
commit
|
commitdiff
|
tree
2019-10-04
Berk Hess
Fix r
a
ndom energy an
d
vi
r
ial with PME
on GPU
on a
P
ME
.
.
.
commit
|
commitdiff
|
tree
2019-10-03
Berk H
e
ss
F
ix
G
PU atom data in
i
t timer issue
commit
|
commitdiff
|
tree
2019-10-03
Berk Hess
Use gmx
:
:Ra
n
ge f
o
r
iZo
n
es i
n
pair search
commit
|
commitdiff
|
tree
2019-10-03
Berk Hess
Fix setting maxNumColumns in Nbnxm:
:
GridSet
commit
|
commitdiff
|
tree
2019-10-02
Ber
k
Hess
Fix harmless OpenMP write race
commit
|
commitdiff
|
tree
2019-10-01
B
e
r
k
Hess
Use g
m
x::Range
i
n domdec
commit
|
commitdiff
|
tree
2019-10-01
Be
r
k Hess
Comp
l
etely remove charge
group
s
commit
|
commitdiff
|
tree
2019-10-01
Berk Hess
S
i
mplify DD exclusion c
o
unting
commit
|
commitdiff
|
tree
2019-10-01
Berk Hess
A
l
ways
o
ut
p
ut
c
o
rrect
kin
e
tic at last step
commit
|
commitdiff
|
tree
2019-09-30
Be
r
k Hes
s
Re
m
ove charge group code from forcerec
commit
|
commitdiff
|
tree
2019-09-30
B
erk Hess
A
c
tually fix g
m
x wha
m
w
ith angl
e
geometries
commit
|
commitdiff
|
tree
2019-09-29
Berk Hess
Increase ti3p5 minimiza
t
ion test tol
e
rance
commit
|
commitdiff
|
tree
2019-09-28
Berk Hess
Fix
C
G
minimizati
o
n with DD
commit
|
commitdiff
|
tree
2019-09-27
Berk Hess
Extract gmx::Range
commit
|
commitdiff
|
tree
2019-09-27
Berk
Hess
F
i
x location of angle in vsi
t
e figure
commit
|
commitdiff
|
tree
2019-09-26
B
erk Hess
Made mdrun appe
n
ding work
again
commit
|
commitdiff
|
tree
2019-09-24
Berk H
e
s
s
Remov
e
obsolete dd_g
e
t_ns_ranges()
commit
|
commitdiff
|
tree
next