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Cosmetic fixes to mdp documentation
2018-05-24
Be
r
k H
e
ss
F
i
x grompp bug w
i
th blocks
o
f same mo
l
ecules
commit
|
commitdiff
|
tree
2018-05-24
Berk H
e
ss
S
implify
i
def_fe
in calc
_
l
i
ste
d
_
l
ambda
commit
|
commitdiff
|
tree
2018-05-24
Berk H
e
ss
C
hange nbs in
n
bv to std::unique
commit
|
commitdiff
|
tree
2018-05-24
Berk Hess
Convert gmx_domdec
_
master_t to
C
+
+
commit
|
commitdiff
|
tree
2018-05-23
Berk Hess
Split off
colle
c
t
.
c
pp
f
rom domdec
.
cpp
commit
|
commitdiff
|
tree
2018-05-23
Ber
k
Hess
Convert nbnxn_se
a
rc
h
to C
+
+
commit
|
commitdiff
|
tree
2018-05-22
Berk Hess
Change
n
b
nxn gr
i
d reallocation
commit
|
commitdiff
|
tree
2018-05-22
Berk Hess
Use std::vector in n
b
n
xn_sear
c
h
_t
commit
|
commitdiff
|
tree
2018-05-22
Berk Hess
Use std
:
:vecto
r
in nbnxn_gri
d
_t
commit
|
commitdiff
|
tree
2018-05-18
Berk
H
es
s
Clean up
in n
b
nxn_grid
.
cpp
commit
|
commitdiff
|
tree
2018-05-17
Berk
H
ess
S
plit off domdec distribution
a
n
d cel
l
size
s
commit
|
commitdiff
|
tree
2018-05-17
Berk H
e
ss
S
pl
i
t atom redistribution off from domde
c
.
cpp
commit
|
commitdiff
|
tree
2018-05-17
Ber
k
Hess
R
e
move commre
c
from set_ddbox
(
)
commit
|
commitdiff
|
tree
2018-05-15
Berk Hess
Clean up PME do
m
ain count pas
s
ing
commit
|
commitdiff
|
tree
2018-05-03
Berk Hess
Enable SIM
D
v
e
rsion of update
commit
|
commitdiff
|
tree
2018-04-27
Berk
Hess
Rem
o
ve pu
l
l MPI
c
ode dupli
c
atio
n
commit
|
commitdiff
|
tree
2018-04-24
Be
r
k Hess
Fix ind
e
xing i
s
sue
i
n
the pull
code
commit
|
commitdiff
|
tree
2018-04-16
Berk Hess
Move natoms_mol out o
f
gmx
_
mo
l
b
l
o
c
k_t
commit
|
commitdiff
|
tree
2018-04-09
Berk Hess
Convert gmx
_
molblock_t to C+
+
commit
|
commitdiff
|
tree
2018-04-03
Berk Hess
Co
n
vert
g
mx_
m
top_t
to
C++
commit
|
commitdiff
|
tree
2018-04-03
Berk Hess
C
h
ange warninp filenm to
s
t
d
::st
r
i
n
g
commit
|
commitdiff
|
tree
2018-04-03
Berk Hess
Do not calculate COM f
o
r
pull group
0
commit
|
commitdiff
|
tree
2018-03-29
Berk
H
ess
Mo
v
e
file
opening
ou
t
of init_pull
(
)
commit
|
commitdiff
|
tree
2018-03-29
B
erk H
e
ss
Modularize pull_coord_
w
o
r
k_t
commit
|
commitdiff
|
tree
2018-03-28
Be
r
k
Hess
R
e
move m
o
ls
f
rom gm
x
_mt
o
p
_
t
commit
|
commitdiff
|
tree
2018-03-20
Ber
k
Hess
F
i
x gmx dum
p
AWH formatting
i
ssue
commit
|
commitdiff
|
tree
2018-03-20
Berk
H
ess
Disallow single simulation with
multisim
commit
|
commitdiff
|
tree
2018-03-16
Berk Hes
s
C
o
rrect
P
M
F sign
e
rror
i
n A
W
H bias shar
i
ng
commit
|
commitdiff
|
tree
2018-03-16
Berk Hess
F
i
x
r
ecent mdrun si
g
na
l
i
ng
b
ug
commit
|
commitdiff
|
tree
2018-03-15
B
e
r
k
Hes
s
Fix virial with ext
e
rnal p
u
l
l
potentia
l
an
d
MP
I
commit
|
commitdiff
|
tree
2018-03-14
Berk Hess
Improve in
t
er-
s
imulation signaling
commit
|
commitdiff
|
tree
2018-03-14
Berk Hess
Fix mdrun sign
a
ll
i
ng with AWH b
i
as sharing
commit
|
commitdiff
|
tree
2018-03-14
Berk Hess
F
i
x COM
pulling
w
ith ext
e
rnal po
t
ential w
i
th
#ranks>32
commit
|
commitdiff
|
tree
2018-03-14
B
erk Hess
Fi
x
pull bug
w
ith geometry=direction-periodic
commit
|
commitdiff
|
tree
2018-03-13
Berk Hess
Add A
W
H
f
ix
e
s
to
r
ele
a
se
n
o
tes
commit
|
commitdiff
|
tree
2018-03-13
Berk Hess
Fix AWH e
n
semble chec
k
p
o
i
n
ting
commit
|
commitdiff
|
tree
2018-03-13
Berk Hess
Fix
A
WH deconvo
l
uti
o
n when sharing a bia
s
commit
|
commitdiff
|
tree
2018-03-09
Be
r
k He
s
s
Correct pdb2gmx -m
i
ssing op
t
ion
commit
|
commitdiff
|
tree
2018-03-07
Berk Hess
Fix memory leak in PM
E
commit
|
commitdiff
|
tree
2018-03-06
Berk He
s
s
Convert
t
_
fi
l
enm t
o
C
+
+
commit
|
commitdiff
|
tree
2018-03-06
Berk
H
e
ss
Ma
k
e
multi-a
t
om TPI
r
e
p
r
o
d
u
cib
l
e
commit
|
commitdiff
|
tree
2018-03-05
Berk Hess
Wor
k
a
r
oun
d
gcc bug w
i
th group
kernel ta
b
les
commit
|
commitdiff
|
tree
2018-03-05
B
erk Hess
Leave nul
l
p
t
r opt
i
n
t
_
filenm
commit
|
commitdiff
|
tree
2018-03-02
Berk Hess
Fix cppch
e
ck
w
arning
commit
|
commitdiff
|
tree
2018-03-02
Berk Hess
Fix AWH
bias-sha
r
ing with parallel simulatio
n
commit
|
commitdiff
|
tree
2018-03-01
Berk He
s
s
Detect A
M
D
SMT topology
commit
|
commitdiff
|
tree
2018-03-01
Berk Hes
s
Fix mdrun m
u
ltisim wi
t
h s
e
parate PM
E
ranks
commit
|
commitdiff
|
tree
2018-02-23
Berk Hess
F
ix md integrator with Nose-Hoover coupling
commit
|
commitdiff
|
tree
2018-02-22
Be
r
k Hes
s
Simplify mdrun
tMPI t
h
re
a
d sp
a
wning
commit
|
commitdiff
|
tree
2018-02-16
Berk Hess
Correct multisim MP
I
barrier
commit
|
commitdiff
|
tree
2018-02-14
Berk Hes
s
Remove s
u
pport for
tp
x
vers
i
on before 58
/
gmx4
.
0
commit
|
commitdiff
|
tree
2018-02-14
B
erk Hess
Fix range b
u
g in add_select
i
on_groups
in tngio
.
cpp
commit
|
commitdiff
|
tree
2018-02-14
Berk He
s
s
Fix gromp
p
net cha
r
ge chec
k
commit
|
commitdiff
|
tree
2018-02-14
Berk Hess
Fix grompp net
charge check
commit
|
commitdiff
|
tree
2018-02-08
B
e
rk Hess
U
se SIMD bondeds
w
ithout perturbed i
n
teractions
commit
|
commitdiff
|
tree
2018-02-08
Berk Hes
s
Allow bonds with distance=0
commit
|
commitdiff
|
tree
2018-02-05
Be
r
k Hess
Set cutof
f
m
o
difie
r
s
in
forcer
e
c
commit
|
commitdiff
|
tree
2018-02-05
Berk Hess
Fix
a
sser
t
io
n
failure i
n
T
P
I
commit
|
commitdiff
|
tree
2018-01-30
Berk Hess
Removed
unused
f
lag
PCA_CAN_R
E
A
D
_NODE
commit
|
commitdiff
|
tree
2018-01-18
Berk
H
ess
Fix COMM remo
v
al on part of the system
commit
|
commitdiff
|
tree
2018-01-18
B
erk Hess
Add
c
heck
i
n grom
p
p t
o
a
v
oid asser
t
ion failure
commit
|
commitdiff
|
tree
2018-01-17
Berk Hess
Re
p
lace
s
tderr
p
rints
i
n
filenm
.
cpp by
a
sserts
commit
|
commitdiff
|
tree
2018-01-17
Berk
H
ess
Re-e
n
abl
e
GPU w
i
th walls and 1
energy group
commit
|
commitdiff
|
tree
2018-01-16
Berk
Hes
s
Remove
t
umbling ice-cub
e
warnin
g
with SD
commit
|
commitdiff
|
tree
2018-01-16
Berk Hess
A
vo
i
d mdrun echoin
g
"No o
p
tion -multi"
commit
|
commitdiff
|
tree
2018-01-09
Ber
k
Hess
R
e
word
CPU/GPU imbalance notes
commit
|
commitdiff
|
tree
2018-01-09
Berk
H
es
s
Do not turn on DLB at r
e
plica ex
c
hange
commit
|
commitdiff
|
tree
2018-01-08
Berk He
s
s
Fix triclinic domain deco
m
p
o
sition bug
commit
|
commitdiff
|
tree
2017-12-19
Berk Hess
M
ake ac
c
elera
t
ion
c
orrection VC
M
m
o
de w
o
rk
commit
|
commitdiff
|
tree
2017-12-19
Be
r
k
H
e
s
s
Make
ov
e
rsubscr
i
pt
i
on warning c
o
nsistent
commit
|
commitdiff
|
tree
2017-12-14
Berk Hess
Require
-ntmpi with setting -ntom
p
with GPUs
commit
|
commitdiff
|
tree
2017-12-12
Berk Hess
C
heck for la
r
ge
energy at first st
e
p
commit
|
commitdiff
|
tree
2017-12-12
Berk Hess
Avo
i
d yelling about thread pi
n
ning twice
commit
|
commitdiff
|
tree
2017-12-11
Berk Hes
s
A
d
d grompp
note for
PR pcoup
l
e + po
s
i
t
ion restraints
commit
|
commitdiff
|
tree
2017-12-10
Berk Hess
Remove SIMD warning for A
M
D Zen
commit
|
commitdiff
|
tree
2017-12-10
Berk He
s
s
Tone down note
about not pinning threads
commit
|
commitdiff
|
tree
2017-12-08
Be
r
k
Hess
Correc
t
Shake
test to
l
erances
commit
|
commitdiff
|
tree
2017-12-08
Berk He
s
s
A
dd Viveca
L
indahl as contribu
t
or
commit
|
commitdiff
|
tree
2017-12-07
Berk
H
ess
C
hoose faster nbnxn SIMD kernels on AMD Zen
commit
|
commitdiff
|
tree
2017-12-05
Berk Hess
Fix DD
exact cont
i
nuation bug
commit
|
commitdiff
|
tree
2017-12-04
B
er
k
Hess
Fix pme gather in double wi
t
h AVX(2)_1
2
8
commit
|
commitdiff
|
tree
2017-12-04
Berk He
s
s
Merge "Merge b
r
anc
h
release-
2
016 i
n
to rel
e
ase-2018
.
.
.
commit
|
commitdiff
|
tree
2017-12-04
Berk
He
s
s
F
i
xed in
i
tial temperature reporti
n
g
commit
|
commitdiff
|
tree
2017-12-04
B
e
rk Hess
Up
d
ate mdrun
s
ignal help text
commit
|
commitdiff
|
tree
2017-12-04
Be
r
k Hess
Only sto
p
a
t nstlist
s
teps with -repr
o
d
commit
|
commitdiff
|
tree
2017-12-03
B
e
rk Hess
Clear vsite vel
o
cities fo
r
simple in
t
egrators
commit
|
commitdiff
|
tree
2017-12-03
Berk Hess
Ti
g
hte
n
B-spl
i
ne moduli sin
g
le pre
c
ision
t
e
s
t tolerance
.
.
.
commit
|
commitdiff
|
tree
2017-12-02
Berk Hess
Avoid assertion
f
a
i
lure in AWH
commit
|
commitdiff
|
tree
2017-11-29
Berk Hes
s
Ch
a
nge t
h
e GPU
S
MT
cut-o
f
f to quadratic
commit
|
commitdiff
|
tree
2017-11-28
Berk
Hess
Update documention of Nose-H
o
over output
commit
|
commitdiff
|
tree
2017-11-28
Berk Hess
R
efact
o
r n
b
nxn exclusio
n
setting
commit
|
commitdiff
|
tree
2017-11-28
B
erk Hess
Extend grompp missing
e
n
e
rgy
t
e
rm message
commit
|
commitdiff
|
tree
2017-11-27
B
erk H
e
ss
Enable auto thr
e
ad pi
n
ni
n
g
wit
h
thread limiting
commit
|
commitdiff
|
tree
2017-11-27
Berk Hes
s
Fix
P
ME GPU with walls
commit
|
commitdiff
|
tree
2017-11-25
B
erk
Hess
Fix compiler w
a
rnin
g
with
o
ut MPI
commit
|
commitdiff
|
tree
2017-11-24
Berk Hess
Disable
d
C
U
D
A
timing
s
commit
|
commitdiff
|
tree
2017-11-24
Ber
k
Hess
S
p
eed up nbnxn buf
f
er cl
e
aring
commit
|
commitdiff
|
tree
2017-11-24
B
e
rk
H
ess
Limit SMT
w
ith PME on GPU
commit
|
commitdiff
|
tree
2017-11-23
Berk Hes
s
Up
d
a
te
n
ote in manual on SD
commit
|
commitdiff
|
tree
2017-11-23
Ber
k
Hess
Correct
P
ME GPU timing
n
a
m
ing
commit
|
commitdiff
|
tree
next