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
Fix warnings with clang 9
2020-04-06
Berk Hess
M
o
v
e
force buf
f
er resizing
to mdsetup
commit
|
commitdiff
|
tree
2020-03-20
Berk Hess
Rename c
l
a
ss G
r
id
t
o
BiasG
r
id in AWH
modul
e
commit
|
commitdiff
|
tree
2020-03-19
Berk
H
ess
Simplify f
i
nish_u
p
date()
commit
|
commitdiff
|
tree
2020-03-19
Berk Hess
Remo
v
e at_st
a
rt from t_graph
commit
|
commitdiff
|
tree
2020-03-18
B
e
rk He
s
s
R
emove use of graph in
do_force()
commit
|
commitdiff
|
tree
2020-03-18
Berk Hess
Use WholeMo
l
ec
u
leTransf
o
rm f
o
r orires and ep
s
il
o
n
-s
u
rf
a
ce
commit
|
commitdiff
|
tree
2020-03-18
Berk
Hess
Add W
h
oleMoleculeTrans
f
or
m
class
commit
|
commitdiff
|
tree
2020-03-17
Berk Hess
Convert
t_
g
raph to C++
commit
|
commitdiff
|
tree
2020-03-13
Berk Hess
Add t
e
sts for
Ewald surf
a
ce terms
commit
|
commitdiff
|
tree
2020-03-11
Berk Hess
Add
tests
f
or
gr
a
ph
commit
|
commitdiff
|
tree
2020-03-10
B
e
r
k
H
e
ss
Fix
t
y
pe in rang
e
a
n
d add tests
commit
|
commitdiff
|
tree
2020-03-07
Berk Hess
Make
s
hake work witho
u
t
g
rap
h
commit
|
commitdiff
|
tree
2020-03-05
Berk Hess
Add Interaction
D
efinitions
commit
|
commitdiff
|
tree
2020-03-02
Berk Hess
Fix ce
n
ter of mass motion r
e
moval with froz
e
n
atoms
commit
|
commitdiff
|
tree
2020-03-02
Berk He
s
s
Fix grompp unb
o
und ato
m
check
commit
|
commitdiff
|
tree
2020-03-02
Berk Hess
F
i
x nrdf
w
ith partial COMM removal
commit
|
commitdiff
|
tree
2020-03-02
Berk Hess
F
ix
too small pairlist buffer on Intel GPUs
commit
|
commitdiff
|
tree
2020-02-21
Berk Hess
Add fatal error wh
e
n
multisim runs sha
r
ing
st
a
te
h
ave
.
.
.
commit
|
commitdiff
|
tree
2020-02-15
Berk
H
e
s
s
R
em
o
ve 1 p
u
l
se
D
D
re
q
uest
commit
|
commitdiff
|
tree
2020-02-05
Berk Hess
Actua
l
ly fix P
M
E for
c
es with FE without perturbed q/LJ
commit
|
commitdiff
|
tree
2020-02-04
Be
r
k H
e
ss
A
ctually
f
ix
PME forc
e
s with F
E
with
o
ut
p
ert
u
rbed q/LJ
commit
|
commitdiff
|
tree
2020-01-23
Be
r
k
He
s
s
Fix DD rank count prim
e
check
commit
|
commitdiff
|
tree
2020-01-22
B
e
rk Hess
Minor cleanup in constraint and shell
f
c
cod
e
commit
|
commitdiff
|
tree
2020-01-22
Berk Hess
Fix il
l
e
gal memory a
c
cess in PME co
m
municati
o
n
commit
|
commitdiff
|
tree
2020-01-22
B
e
rk He
s
s
Clar
i
fy COM
M
/posr
e
s grompp note
commit
|
commitdiff
|
tree
2020-01-20
Berk Hess
Use
ArrayRef(W
i
thPad
d
i
ng) in con
s
traint co
d
e
commit
|
commitdiff
|
tree
2020-01-20
B
erk
H
ess
Use
s
td::vector i
n
shel
l
fc
commit
|
commitdiff
|
tree
2020-01-17
Berk H
e
ss
Add
c
heck f
o
r shells and GPU update
commit
|
commitdiff
|
tree
2020-01-16
Berk Hess
Cor
r
ect fixed redmine issue
i
d
f
r
o
m 32
9
7 to 3296
commit
|
commitdiff
|
tree
2020-01-15
Berk Hess
Fix multisi
m
w
i
t
h
paralle
l
simulation
commit
|
commitdiff
|
tree
2020-01-13
Berk Hess
Avoid unne
c
essary exclusion ge
n
eration in DD
commit
|
commitdiff
|
tree
2019-12-22
B
erk Hess
Use ListOfLists for atom to c
o
n
s
traint mappin
g
commit
|
commitdiff
|
tree
2019-12-22
Berk Hes
s
Mov
e
n
r
_nonperturb
e
d
out of
t
_ilis
t
commit
|
commitdiff
|
tree
2019-12-19
B
e
rk Hess
Expand ListOfLi
s
ts pus
h
Back(
)
functionality
commit
|
commitdiff
|
tree
2019-12-19
B
e
rk Hess
Remove
ex
c
lusions f
r
om t_topology
commit
|
commitdiff
|
tree
2019-12-19
Berk Hess
Fix mdrun appending invalidat
i
ng
e
n
e
rgy fi
l
e
s
commit
|
commitdiff
|
tree
2019-12-18
Berk Hess
C
hange grompp decoup
l
ing SD w
a
rning to note
commit
|
commitdiff
|
tree
2019-12-17
Berk Hess
Add n
o
t
e for COM removal
wi
t
h position re
s
trai
n
ts
commit
|
commitdiff
|
tree
2019-12-16
Berk Hess
Use ListOfLis
t
s in
gmx_mto
p
_t and
g
mx_loc
a
lt
o
p_
t
commit
|
commitdiff
|
tree
2019-12-16
Berk Hess
Fi
x
issues
i
n
L
is
t
OfLists
commit
|
commitdiff
|
tree
2019-12-12
Berk
Hess
Add class
L
i
s
t
OfLists
commit
|
commitdiff
|
tree
2019-12-02
Berk Hess
Add
c
heck for coupled
constraint
s
for CUDA upda
t
e
commit
|
commitdiff
|
tree
2019-12-02
Berk Hess
Extract
L
INC
S
CUDA
h
elper funct
i
o
n
s
commit
|
commitdiff
|
tree
2019-11-29
Berk Hes
s
Merge "Merge branch rele
a
se
-
2019 i
n
to releas
e
-2020
.
.
.
commit
|
commitdiff
|
tree
2019-11-28
Berk He
s
s
Update do
c
um
e
n
a
tion for N
P
T GP
U
update
commit
|
commitdiff
|
tree
2019-11-28
Ber
k
Hess
Remove a
s
sertion failure in AWH with
o
ut in
i
tial
s
tage
commit
|
commitdiff
|
tree
2019-11-28
B
erk Hess
Fix bug with GPU pressure
s
caling at non T
-
scal
i
n
g
.
.
.
commit
|
commitdiff
|
tree
2019-11-26
Ber
k
Hess
Fix is
s
ues with AWH
w
i
th period
i
c pulling
commit
|
commitdiff
|
tree
2019-11-20
B
erk Hess
Qu
i
e
t pdb2g
m
x
a
nd use gmx_fatal
commit
|
commitdiff
|
tree
2019-11-19
Be
r
k Hess
Fix bonded
a
t
o
m commun
i
cation pe
r
forma
n
ce
commit
|
commitdiff
|
tree
2019-11-18
B
erk
H
e
s
s
Fix intermolecular interaction
s
with
DD
commit
|
commitdiff
|
tree
2019-11-14
Berk Hess
Sim
p
lify
t_forcerec destr
u
ction
commit
|
commitdiff
|
tree
2019-11-07
Berk Hess
Fix
.
g
r
o la
r
g
e
box wri
t
ing
commit
|
commitdiff
|
tree
2019-11-06
Berk He
s
s
D
eprecate
d
s
c-r-power=48
commit
|
commitdiff
|
tree
2019-11-01
Berk Hess
Add ha
v
e
E
waldSurfaceContrib
u
ti
o
n to Si
m
ulationWorkl
o
ad
commit
|
commitdiff
|
tree
2019-10-31
Berk He
s
s
Update GPU up
d
ate
restrictions
commit
|
commitdiff
|
tree
2019-10-30
Berk Hes
s
Fix wall
s
with GPU u
p
d
ate
commit
|
commitdiff
|
tree
2019-10-29
Berk Hes
s
Add mdrun GPU update docu
m
e
n
tation
commit
|
commitdiff
|
tree
2019-10-29
B
erk Hess
Fix
Ewald dipole corre
c
tio
n
w
i
t
h
GPU update
commit
|
commitdiff
|
tree
2019-10-29
Ber
k
Hess
Disa
b
le pressure coupling with GPU
update
commit
|
commitdiff
|
tree
2019-10-24
Berk He
s
s
Add bool useDomainDe
c
omposition in m
d
runner
commit
|
commitdiff
|
tree
2019-10-24
Be
r
k Hess
A
dd gmx_mtop_inte
r
acti
o
n
_co
u
nt
(
)
commit
|
commitdiff
|
tree
2019-10-24
Berk Hes
s
Fix initia
l
izers in
l
ocal
i
t
y
.
h
commit
|
commitdiff
|
tree
2019-10-23
B
e
r
k Hess
Mo
v
e
l
ocality
.
h from nbnxm to m
d
t
ypes
commit
|
commitdiff
|
tree
2019-10-23
Be
r
k Hess
Use
gmx::
R
ange in Nbnx
m
gri
d
ding fu
n
ctions
commit
|
commitdiff
|
tree
2019-10-23
Berk Hess
Fix
illegal memo
r
y
a
ccess in FE calc
u
lations
commit
|
commitdiff
|
tree
2019-10-23
Berk Hess
Ex
p
and docum
e
ntation f
o
r nbnxn_pu
t
_o
n
_gri
d
()
commit
|
commitdiff
|
tree
2019-10-22
Berk H
e
ss
R
e
quire
-ei for
e
sse
n
t
ia
l
dynamics
commit
|
commitdiff
|
tree
2019-10-18
Berk Hess
Upd
a
t
e grompp
c
ut
o
ff-sch
e
me warnings
commit
|
commitdiff
|
tree
2019-10-15
Berk Hess
Const
correctness for gen
h
ydr
o
commit
|
commitdiff
|
tree
2019-10-12
Berk
H
es
s
Add class FixedCapacit
y
Vector
commit
|
commitdiff
|
tree
2019-10-09
B
e
rk Hess
Incre
a
se spc minim
i
zation test tolerance
commit
|
commitdiff
|
tree
2019-10-09
B
erk Hess
Fix ha
r
ml
e
ss
O
p
e
n
M
P write race
commit
|
commitdiff
|
tree
2019-10-09
Berk
H
es
s
Fix GPU atom
data init ti
m
e
r issue
commit
|
commitdiff
|
tree
2019-10-09
Ber
k
Hess
Fix random energy
a
nd virial with PME on
GPU
on
a PME
.
.
.
commit
|
commitdiff
|
tree
2019-10-08
B
e
rk
Hess
Make nbnxm
a pro
p
er
m
odule
commit
|
commitdiff
|
tree
2019-10-08
Berk H
e
ss
S
implify ewa
l
d_LRcorr
e
ction() cal
l
si
g
nature
commit
|
commitdiff
|
tree
2019-10-04
Berk H
e
s
s
Fix
r
a
ndo
m
energy and virial w
i
th PME on GPU on a PME
.
.
.
commit
|
commitdiff
|
tree
2019-10-03
Berk Hess
F
ix GPU
atom data init timer issue
commit
|
commitdiff
|
tree
2019-10-03
B
e
rk Hess
U
s
e
g
m
x:
:
R
a
nge for iZones in
pair
s
earch
commit
|
commitdiff
|
tree
2019-10-03
Berk H
e
ss
F
ix
sett
i
ng maxNumColumns in N
b
nxm::Gr
i
dSet
commit
|
commitdiff
|
tree
2019-10-02
Berk Hess
Fix ha
r
mless Ope
n
M
P
wr
i
te race
commit
|
commitdiff
|
tree
2019-10-01
Berk
H
ess
Use gmx::Ran
g
e in do
m
dec
commit
|
commitdiff
|
tree
2019-10-01
Berk He
s
s
Comp
l
etely
remove charge gr
o
u
p
s
commit
|
commitdiff
|
tree
2019-10-01
Berk H
e
ss
Simpl
i
f
y DD exclusion counting
commit
|
commitdiff
|
tree
2019-10-01
Berk Hess
Alw
a
ys
output
c
orrect
k
ineti
c
at
l
ast step
commit
|
commitdiff
|
tree
2019-09-30
Be
r
k Hess
Re
m
ove
charge group code from forcere
c
commit
|
commitdiff
|
tree
2019-09-30
Berk Hess
Actually f
i
x gmx w
h
am wi
t
h angle geo
m
etries
commit
|
commitdiff
|
tree
2019-09-29
Be
r
k Hess
Increase ti3p5 minimization t
e
st tolerance
commit
|
commitdiff
|
tree
2019-09-28
Berk Hess
Fix C
G
mini
m
ization with DD
commit
|
commitdiff
|
tree
2019-09-27
Berk H
e
ss
Ex
t
ract gmx::
R
an
g
e
commit
|
commitdiff
|
tree
2019-09-27
Berk Hess
Fix lo
c
ation of angle
in vsite figure
commit
|
commitdiff
|
tree
2019-09-26
Berk Hess
Made mdrun appending work again
commit
|
commitdiff
|
tree
2019-09-24
Berk H
e
ss
Re
m
ov
e
obsolete
d
d
_
get_ns_ranges()
commit
|
commitdiff
|
tree
2019-09-23
Berk Hess
L
imit Z
e
n
nbnxm ke
r
nel
c
hoice t
o
Zen 1
commit
|
commitdiff
|
tree
2019-09-22
Ber
k
He
s
s
Remove cgs_gl from gmx_domdec_co
m
m_t
commit
|
commitdiff
|
tree
2019-09-21
B
e
rk
H
ess
Fi
x
inco
r
r
ect s
h
if
t
forces for CMAP
commit
|
commitdiff
|
tree
2019-09-20
Berk Hess
Fix DD 1 pulse checks without DLB
commit
|
commitdiff
|
tree
2019-09-19
Ber
k
Hess
R
e
move bLoc
a
lCG from DD c
o
de
commit
|
commitdiff
|
tree
2019-09-19
Be
r
k Hess
Remove obsolete make_exclu
s
ion
s
_zone_cg()
commit
|
commitdiff
|
tree
next