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
Enable uncrustify for OpenCL
2018-04-27
Berk He
s
s
Rem
o
v
e
pull M
P
I code du
p
lication
commit
|
commitdiff
|
tree
2018-04-16
Berk
Hess
Move natoms
_
mol out
of
g
mx_molb
l
ock_t
commit
|
commitdiff
|
tree
2018-04-09
Be
r
k Hess
Con
v
ert gmx_m
o
lblock_t to C++
commit
|
commitdiff
|
tree
2018-04-03
Berk Hess
Convert gm
x
_m
t
op_t to C++
commit
|
commitdiff
|
tree
2018-04-03
Berk Hess
Cha
n
ge warninp filenm to st
d
:
:stri
n
g
commit
|
commitdiff
|
tree
2018-04-03
Be
r
k Hess
Do not calculate C
O
M
for pull group 0
commit
|
commitdiff
|
tree
2018-03-29
Berk Hess
M
ove file opening
o
u
t of in
i
t_pull()
commit
|
commitdiff
|
tree
2018-03-29
Berk Hess
Modul
a
rize
pull_co
o
rd_work_
t
commit
|
commitdiff
|
tree
2018-03-28
B
e
rk Hess
Remove
mols from
gmx_mtop
_
t
commit
|
commitdiff
|
tree
2018-03-20
Berk Hes
s
Fix gmx
d
ump AWH formatt
i
ng issue
commit
|
commitdiff
|
tree
2018-03-20
Berk Hess
Disallow
single simu
l
ation with multisim
commit
|
commitdiff
|
tree
2018-03-16
Berk Hess
Correct
PMF si
g
n er
r
or in AWH bias sharing
commit
|
commitdiff
|
tree
2018-03-16
Berk He
s
s
Fix re
c
ent mdr
u
n signaling bug
commit
|
commitdiff
|
tree
2018-03-15
Berk Hess
Fix virial
w
i
th
e
xtern
a
l pull
potential
and MP
I
commit
|
commitdiff
|
tree
2018-03-14
B
e
rk Hess
Imp
r
ove i
n
ter-simulation signaling
commit
|
commitdiff
|
tree
2018-03-14
B
e
r
k Hes
s
F
ix mdrun s
i
gnalling with
A
W
H
bias sharing
commit
|
commitdiff
|
tree
2018-03-14
Berk Hes
s
F
ix COM pu
l
l
ing w
i
th ext
e
rna
l
potential
with #ranks>32
commit
|
commitdiff
|
tree
2018-03-14
B
e
rk H
e
ss
Fi
x
pull bug with
g
eometry=direct
i
on-per
i
od
i
c
commit
|
commitdiff
|
tree
2018-03-13
Berk Hess
Add AWH fixes to
release notes
commit
|
commitdiff
|
tree
2018-03-13
Be
r
k
H
e
ss
Fi
x
AW
H
ense
m
b
l
e
c
heckp
o
inting
commit
|
commitdiff
|
tree
2018-03-13
Berk Hess
Fix AW
H
deconv
o
lu
t
ion when s
h
aring
a
bias
commit
|
commitdiff
|
tree
2018-03-09
Berk He
s
s
Corr
e
c
t
pdb2
g
mx -mi
s
sing option
commit
|
commitdiff
|
tree
2018-03-07
Berk He
s
s
Fix mem
o
ry leak in PME
commit
|
commitdiff
|
tree
2018-03-06
Berk Hess
Conver
t
t
_
f
i
l
e
n
m to
C+
+
commit
|
commitdiff
|
tree
2018-03-06
B
e
rk
Hess
Make
m
ulti-atom TPI
r
eproducible
commit
|
commitdiff
|
tree
2018-03-05
Berk Hess
Work around gcc bug with
g
ro
u
p kernel
t
a
bles
commit
|
commitdiff
|
tree
2018-03-05
Berk
He
s
s
L
e
ave
nullp
t
r o
p
t in t_filenm
commit
|
commitdiff
|
tree
2018-03-02
Berk He
s
s
F
i
x cppcheck warnin
g
commit
|
commitdiff
|
tree
2018-03-02
Berk
H
ess
Fix AWH bi
a
s-shari
n
g
w
ith parallel sim
u
lati
o
n
commit
|
commitdiff
|
tree
2018-03-01
Berk H
e
ss
Detect
AMD SMT topo
l
ogy
commit
|
commitdiff
|
tree
2018-03-01
Berk
Hes
s
Fi
x
mdrun mul
t
isim with sepa
r
ate PME ranks
commit
|
commitdiff
|
tree
2018-02-23
Berk Hess
Fix md integrator w
i
th Nose-Hoover
c
ou
p
ling
commit
|
commitdiff
|
tree
2018-02-22
Berk Hess
S
i
m
pli
f
y mdrun tMPI thread s
p
awni
n
g
commit
|
commitdiff
|
tree
2018-02-16
Berk
Hess
C
o
rrect m
u
l
t
i
sim MPI barrier
commit
|
commitdiff
|
tree
2018-02-14
B
erk He
s
s
Rem
o
ve s
u
p
po
r
t for tpx ver
s
ion before 58/gmx4
.
0
commit
|
commitdiff
|
tree
2018-02-14
Berk Hess
Fix
r
ange b
u
g in
add_s
e
l
e
ction_gr
o
u
p
s i
n
tngio
.
cpp
commit
|
commitdiff
|
tree
2018-02-14
Be
r
k Hess
Fix
gro
m
pp ne
t
charge check
commit
|
commitdiff
|
tree
2018-02-14
Ber
k
H
e
s
s
Fix g
r
ompp
net charge ch
e
ck
commit
|
commitdiff
|
tree
2018-02-08
Berk He
s
s
U
se SIMD bondeds withou
t
pertur
b
ed intera
c
tions
commit
|
commitdiff
|
tree
2018-02-08
Be
r
k
Hes
s
Allow bon
d
s w
i
th
d
i
stance=0
commit
|
commitdiff
|
tree
2018-02-05
Be
r
k Hess
Set cutof
f
modi
f
iers
in forcerec
commit
|
commitdiff
|
tree
2018-02-05
Berk Hess
Fix assertion failure in TPI
commit
|
commitdiff
|
tree
2018-01-30
Berk
He
s
s
Remove
d
unuse
d
flag PCA_CAN_READ_NODE
commit
|
commitdiff
|
tree
2018-01-18
Berk Hess
F
i
x COMM r
e
m
o
val o
n
part
of
t
he system
commit
|
commitdiff
|
tree
2018-01-18
Berk H
e
ss
Add check in grom
p
p to avoid assertion
f
ailure
commit
|
commitdiff
|
tree
2018-01-17
Berk Hes
s
Re
p
lace stderr prints in file
n
m
.
cpp by asserts
commit
|
commitdiff
|
tree
2018-01-17
Berk He
s
s
Re
-
enable GPU wi
t
h wa
l
ls and 1 energy group
commit
|
commitdiff
|
tree
2018-01-16
Ber
k
Hess
Remo
v
e tumbling ic
e
-cube
warning with SD
commit
|
commitdiff
|
tree
2018-01-16
Berk Hes
s
A
v
oi
d
mdrun echoing "No o
p
tion -multi"
commit
|
commitdiff
|
tree
2018-01-09
Berk
H
ess
R
ew
o
rd CPU/G
P
U
imbalance
n
ote
s
commit
|
commitdiff
|
tree
2018-01-09
Berk
H
ess
Do not
t
u
rn on DLB
at replica
e
x
ch
a
nge
commit
|
commitdiff
|
tree
2018-01-08
Berk
H
ess
Fix triclinic dom
a
in
d
ecompos
i
tion bug
commit
|
commitdiff
|
tree
2017-12-19
Berk Hess
M
ak
e
acceleration
correction VCM mode w
o
rk
commit
|
commitdiff
|
tree
2017-12-19
Berk Hess
Mak
e
oversubs
c
r
i
p
tio
n
warni
n
g consi
s
tent
commit
|
commitdiff
|
tree
2017-12-14
Berk Hess
Require -ntmpi wit
h
setting -
n
tomp with GPUs
commit
|
commitdiff
|
tree
2017-12-12
Berk Hes
s
Check for large
energy at fir
s
t step
commit
|
commitdiff
|
tree
2017-12-12
Berk Hess
Avoid yellin
g
a
b
out threa
d
pinn
i
ng
twice
commit
|
commitdiff
|
tree
2017-12-11
Berk Hess
Add gro
m
pp note for PR pcouple + p
o
sition r
e
straint
s
commit
|
commitdiff
|
tree
2017-12-10
Berk
Hess
R
emove SIMD warning for AM
D
Zen
commit
|
commitdiff
|
tree
2017-12-10
Berk Hess
To
n
e down note ab
o
ut
not pinnin
g
threa
d
s
commit
|
commitdiff
|
tree
2017-12-08
Berk H
e
ss
C
or
r
ect Shake test toleranc
e
s
commit
|
commitdiff
|
tree
2017-12-08
B
e
rk Hess
Add Viveca L
i
n
d
a
hl as
c
ont
r
ibutor
commit
|
commitdiff
|
tree
2017-12-07
B
e
rk Hess
Choose faster n
b
n
xn SIMD kernel
s
on AMD Zen
commit
|
commitdiff
|
tree
2017-12-05
B
e
rk Hess
Fix DD exac
t
cont
i
nuation bug
commit
|
commitdiff
|
tree
2017-12-04
Berk
Hess
Fix
p
me gathe
r
i
n
doub
l
e with AVX(2)_
1
28
commit
|
commitdiff
|
tree
2017-12-04
Berk He
s
s
M
erge "Merge branch rele
a
se-2016 into rel
e
ase
-
201
8
.
.
.
commit
|
commitdiff
|
tree
2017-12-04
Berk Hess
Fi
x
ed initial temperature reporting
commit
|
commitdiff
|
tree
2017-12-04
Be
r
k
Hess
Update mdrun signal h
e
lp text
commit
|
commitdiff
|
tree
2017-12-04
Berk Hess
Only stop
a
t
nstli
s
t s
t
ep
s
with -repro
d
commit
|
commitdiff
|
tree
2017-12-03
Berk Hess
C
lear vsite v
e
l
o
cities
f
or simp
l
e
integrators
commit
|
commitdiff
|
tree
2017-12-03
Berk Hess
Ti
g
hten B-spline moduli s
i
ngle
pre
c
ision test tole
r
ance
.
.
.
commit
|
commitdiff
|
tree
2017-12-02
Berk Hess
Avoid assertion fai
l
ure in
A
W
H
commit
|
commitdiff
|
tree
2017-11-29
Berk Hess
Change the GP
U
S
M
T
c
u
t-off to quadrati
c
commit
|
commitdiff
|
tree
2017-11-28
Berk H
e
ss
Update documention of Nos
e
-Hoover ou
t
pu
t
commit
|
commitdiff
|
tree
2017-11-28
Berk Hess
R
e
f
acto
r
nbn
x
n exclusion settin
g
commit
|
commitdiff
|
tree
2017-11-28
Berk He
s
s
Extend grompp missing e
n
ergy t
e
rm message
commit
|
commitdiff
|
tree
2017-11-27
Berk Hess
Enable auto t
h
read p
i
nning with
t
hread li
m
i
t
ing
commit
|
commitdiff
|
tree
2017-11-27
Berk Hes
s
Fix PME GP
U
with
walls
commit
|
commitdiff
|
tree
2017-11-25
Berk Hess
Fix co
m
piler warning without MPI
commit
|
commitdiff
|
tree
2017-11-24
Berk Hess
Di
s
abled CUDA timings
commit
|
commitdiff
|
tree
2017-11-24
Berk Hess
Speed up
nbnxn buffer clearing
commit
|
commitdiff
|
tree
2017-11-24
Berk Hess
Lim
i
t
SMT with
PME on GP
U
commit
|
commitdiff
|
tree
2017-11-23
Ber
k
He
s
s
Update
n
ote in manual o
n
SD
commit
|
commitdiff
|
tree
2017-11-23
B
e
rk Hess
C
orrect P
M
E
GPU t
i
mi
n
g naming
commit
|
commitdiff
|
tree
2017-11-20
Berk Hess
Preve
n
t PME t
u
ning excessive grid scaling
commit
|
commitdiff
|
tree
2017-11-19
B
erk H
e
s
s
Add
SIMD for AWH
commit
|
commitdiff
|
tree
2017-11-16
Berk Hess
A
l
so print 1x1
pair-list s
e
tup to
l
o
g
commit
|
commitdiff
|
tree
2017-11-10
Berk
H
ess
Fix genion
c
harge
s
umm
a
t
ion accura
c
y
commit
|
commitdiff
|
tree
2017-11-02
Be
r
k He
s
s
F
i
x Ekin a
t
ste
p
0
w
ith COM
re
m
ova
l
commit
|
commitdiff
|
tree
2017-11-02
Be
r
k
H
es
s
Ad
d
mis
s
ing Ewald correcti
o
n for pme-
u
ser
commit
|
commitdiff
|
tree
2017-10-30
Berk Hes
s
Remove unused sig
n
parameter from dih_angle()
commit
|
commitdiff
|
tree
2017-10-29
Berk
Hess
R
e
m
ove incor
r
ect com
m
ent for CHARMM tip
s
3p
commit
|
commitdiff
|
tree
2017-10-24
Be
r
k Hes
s
Fix gmx check fo
r
tprs with
diff
e
rent #atoms
commit
|
commitdiff
|
tree
2017-10-23
Berk Hess
Fix inc
o
rrect dV/dlambda
f
or wa
l
ls
commit
|
commitdiff
|
tree
2017-10-21
Ber
k
Hess
Merge
"Merge branch release-20
1
6"
commit
|
commitdiff
|
tree
2017-10-20
Be
r
k
H
ess
Fix
w
arning for co
n
fout wi
t
h per
i
odic molecules
commit
|
commitdiff
|
tree
2017-10-18
Ber
k
He
s
s
Made CUDA PME te
x
ture reference conditio
n
al
commit
|
commitdiff
|
tree
2017-10-15
Berk Hess
Improve vsite parallel ch
e
cking
commit
|
commitdiff
|
tree
2017-10-12
Berk Hess
S
im
p
lify viri
a
l
handling
commit
|
commitdiff
|
tree
2017-10-11
Berk Hess
Disable ARM Neo
n
nativ
e
r
s
q
r
t iter
a
tion
commit
|
commitdiff
|
tree
next