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Convert gmx_mtop_t to C++
2018-04-03
Be
r
k
H
ess
Convert gmx_mtop_t t
o
C++
commit
|
commitdiff
|
tree
2018-04-03
Ber
k
Hess
D
o
not
calculate COM for pull group
0
commit
|
commitdiff
|
tree
2018-03-29
Berk Hess
Move fi
l
e
openin
g
out of in
i
t_pull()
commit
|
commitdiff
|
tree
2018-03-29
Berk Hess
Modularize pul
l
_coord_work_t
commit
|
commitdiff
|
tree
2018-03-28
Berk
H
ess
Re
m
ove mols from gmx_mtop_t
commit
|
commitdiff
|
tree
2018-03-20
Berk Hess
Fix g
m
x du
m
p
AWH formatt
i
ng iss
u
e
commit
|
commitdiff
|
tree
2018-03-20
Berk Hess
Dis
a
llow
single
s
i
m
ula
t
ion with multisim
commit
|
commitdiff
|
tree
2018-03-16
Berk Hes
s
C
o
rrect
P
MF sign error
in AWH bia
s
sharing
commit
|
commitdiff
|
tree
2018-03-16
Berk
Hess
Fix
r
ecent
m
dr
u
n signali
n
g
bug
commit
|
commitdiff
|
tree
2018-03-15
Berk H
e
ss
Fix
v
i
rial
w
i
t
h ex
t
erna
l
pull potential
an
d
MP
I
commit
|
commitdiff
|
tree
2018-03-14
Berk Hess
Im
p
rove
i
nter-simulation signaling
commit
|
commitdiff
|
tree
2018-03-14
B
erk Hess
Fix mdrun sig
n
a
l
ling with AWH bias sha
r
i
ng
commit
|
commitdiff
|
tree
2018-03-14
Berk Hess
Fix COM pulling
wit
h
ex
t
er
n
al potential with #ra
n
ks>32
commit
|
commitdiff
|
tree
2018-03-14
Berk
H
es
s
Fix pull bug wi
t
h geometry=direction-periodic
commit
|
commitdiff
|
tree
2018-03-13
Berk He
s
s
A
d
d
A
W
H fixe
s
to relea
s
e notes
commit
|
commitdiff
|
tree
2018-03-13
Berk Hess
F
i
x AWH ensemble checkp
o
int
i
n
g
commit
|
commitdiff
|
tree
2018-03-13
Berk H
e
ss
Fix AWH deconvolution wh
e
n
sharing a bias
commit
|
commitdiff
|
tree
2018-03-09
Berk Hess
Correct pd
b
2gmx -missing o
p
tion
commit
|
commitdiff
|
tree
2018-03-07
Berk He
s
s
Fix memory l
e
ak in PME
commit
|
commitdiff
|
tree
2018-03-06
Be
r
k
Hess
Convert t_filenm
t
o C++
commit
|
commitdiff
|
tree
2018-03-06
Berk He
s
s
Make multi-atom TPI
reproducible
commit
|
commitdiff
|
tree
2018-03-05
B
erk Hes
s
Work around g
c
c bug with group kernel tables
commit
|
commitdiff
|
tree
2018-03-05
Be
r
k Hess
L
e
ave nullptr opt
i
n t_filenm
commit
|
commitdiff
|
tree
2018-03-02
Berk H
e
ss
Fix
c
ppcheck warning
commit
|
commitdiff
|
tree
2018-03-02
Berk Hess
Fix AWH bi
a
s-sha
r
ing with para
l
lel
simulation
commit
|
commitdiff
|
tree
2018-03-01
Berk He
s
s
De
t
ec
t
AMD SMT topology
commit
|
commitdiff
|
tree
2018-03-01
Ber
k
Hess
Fix mdr
u
n
multisim wit
h
s
eparat
e
PM
E
ranks
commit
|
commitdiff
|
tree
2018-02-23
Berk Hess
F
ix m
d
integ
r
ator with Nose-Hoov
e
r coupli
n
g
commit
|
commitdiff
|
tree
2018-02-22
Berk Hess
Simplify mdrun tMP
I
thread spawnin
g
commit
|
commitdiff
|
tree
2018-02-16
B
erk Hess
Correct multisim MPI barrier
commit
|
commitdiff
|
tree
2018-02-14
B
e
r
k H
e
ss
Remove support for tpx ver
s
ion before 5
8
/gmx
4
.
0
commit
|
commitdiff
|
tree
2018-02-14
Berk Hess
Fix range b
u
g in add_selection_groups in tng
i
o
.
cpp
commit
|
commitdiff
|
tree
2018-02-14
Berk Hess
F
ix gromp
p
n
et charge check
commit
|
commitdiff
|
tree
2018-02-14
Berk Hess
Fix gr
o
mpp net
c
h
a
rge check
commit
|
commitdiff
|
tree
2018-02-08
Berk
H
ess
Use SIMD bon
d
eds wi
t
hout perturbed interac
t
ion
s
commit
|
commitdiff
|
tree
2018-02-08
Berk Hess
Allow bond
s
with distanc
e
=0
commit
|
commitdiff
|
tree
2018-02-05
Berk Hess
Set cutof
f
m
o
dif
i
ers i
n
f
orcerec
commit
|
commitdiff
|
tree
2018-02-05
B
e
rk Hess
Fix as
s
e
rtion failu
r
e in TP
I
commit
|
commitdiff
|
tree
2018-01-30
Berk Hess
Remove
d
unused flag PCA_CAN_R
E
AD_NODE
commit
|
commitdiff
|
tree
2018-01-18
B
erk He
s
s
Fix COM
M
r
e
mova
l
on part of
the syste
m
commit
|
commitdiff
|
tree
2018-01-18
Ber
k
Hess
Add c
h
e
ck i
n
g
ro
m
p
p
to avo
i
d
a
ss
e
rtion failure
commit
|
commitdiff
|
tree
2018-01-17
B
e
rk Hess
Replace stderr
p
rints
in
f
il
e
n
m
.
cpp
by
a
sserts
commit
|
commitdiff
|
tree
2018-01-17
B
e
rk Hess
Re
-
enab
l
e GPU
w
ith walls and
1
e
nergy
g
roup
commit
|
commitdiff
|
tree
2018-01-16
Berk Hess
Remove tumbling
ice-cube wa
r
ni
n
g with SD
commit
|
commitdiff
|
tree
2018-01-16
Be
r
k Hess
Avoid mdrun ech
o
ing "No o
p
tion -
m
u
l
t
i"
commit
|
commitdiff
|
tree
2018-01-09
B
e
rk
H
e
s
s
Reword C
P
U/GPU
imbal
a
nce
notes
commit
|
commitdiff
|
tree
2018-01-09
Be
r
k Hess
Do not t
u
rn on DLB at replic
a
e
xchange
commit
|
commitdiff
|
tree
2018-01-08
B
e
rk H
e
s
s
F
ix triclinic d
o
main
d
e
c
omposit
i
o
n
bug
commit
|
commitdiff
|
tree
2017-12-19
Berk Hess
Make a
c
celerati
o
n correction VCM mode wor
k
commit
|
commitdiff
|
tree
2017-12-19
Berk Hess
Make over
s
ubscr
i
p
t
i
on warn
i
ng con
s
istent
commit
|
commitdiff
|
tree
2017-12-14
Berk Hess
Require
-
n
t
m
pi with
s
et
t
ing -ntomp with GPUs
commit
|
commitdiff
|
tree
2017-12-12
Berk Hess
Check for large energy at first step
commit
|
commitdiff
|
tree
2017-12-12
Berk
Hess
Avoid
y
elling about thread pi
n
ning
t
w
ice
commit
|
commitdiff
|
tree
2017-12-11
B
e
rk Hess
Add grompp n
o
te for PR p
c
ou
p
le + position rest
r
aints
commit
|
commitdiff
|
tree
2017-12-10
Be
r
k Hess
Remove SIMD
warni
n
g for AMD Ze
n
commit
|
commitdiff
|
tree
2017-12-10
Ber
k
Hess
Ton
e
down n
o
te abo
u
t not pinn
i
ng threads
commit
|
commitdiff
|
tree
2017-12-08
Berk
H
es
s
Correct Shake
test
t
olerances
commit
|
commitdiff
|
tree
2017-12-08
Berk H
e
ss
Add
V
i
v
e
c
a Lin
d
ahl as con
t
rib
u
tor
commit
|
commitdiff
|
tree
2017-12-07
Berk Hess
Ch
o
ose f
a
ster
n
bnx
n
SIMD
k
ern
e
ls on AMD Zen
commit
|
commitdiff
|
tree
2017-12-05
B
er
k
Hess
Fix
DD exact conti
n
uation bug
commit
|
commitdiff
|
tree
2017-12-04
Berk Hes
s
F
i
x pm
e
gather in dou
b
le wi
t
h AVX(2)_128
commit
|
commitdiff
|
tree
2017-12-04
Berk
Hess
Merge "M
e
rge branc
h
r
e
l
ease-2016 int
o
r
e
lease-2018
.
.
.
commit
|
commitdiff
|
tree
2017-12-04
Berk Hess
F
i
xe
d
initia
l
t
e
mperature repor
t
i
n
g
commit
|
commitdiff
|
tree
2017-12-04
Berk He
s
s
Updat
e
mdrun sig
n
al he
l
p text
commit
|
commitdiff
|
tree
2017-12-04
Berk Hess
On
l
y
s
to
p
at nstlist steps wi
t
h -reprod
commit
|
commitdiff
|
tree
2017-12-03
Berk Hess
C
l
e
a
r vsite velocities for simple integrators
commit
|
commitdiff
|
tree
2017-12-03
Berk
H
ess
Tighten B-spline mod
u
li single precisi
o
n test tolerance
.
.
.
commit
|
commitdiff
|
tree
2017-12-02
Berk Hess
Avoid assertion failure in AWH
commit
|
commitdiff
|
tree
2017-11-29
B
e
rk Hess
Change the GPU SMT
cut
-
off to quadrat
i
c
commit
|
commitdiff
|
tree
2017-11-28
Berk Hess
Up
d
ate documen
t
ion of No
s
e-Hoov
e
r
outp
u
t
commit
|
commitdiff
|
tree
2017-11-28
Berk Hess
Refacto
r
nbnxn excl
u
sio
n
setting
commit
|
commitdiff
|
tree
2017-11-28
Ber
k
H
ess
Extend grompp missing energy t
e
rm
message
commit
|
commitdiff
|
tree
2017-11-27
Berk H
e
ss
E
nable a
u
to thread pinning
w
ith thr
e
ad
limiting
commit
|
commitdiff
|
tree
2017-11-27
Berk
Hess
Fix
PME GPU with
wal
l
s
commit
|
commitdiff
|
tree
2017-11-25
B
e
rk H
e
ss
Fix compi
l
er warning
without
M
PI
commit
|
commitdiff
|
tree
2017-11-24
Be
r
k Hess
Disabled CUDA timi
n
g
s
commit
|
commitdiff
|
tree
2017-11-24
Berk Hess
S
p
eed up n
b
n
x
n bu
f
fer clearing
commit
|
commitdiff
|
tree
2017-11-24
Be
r
k
H
ess
Limit SMT w
i
th PME on GPU
commit
|
commitdiff
|
tree
2017-11-23
Berk Hes
s
Update note in manual on SD
commit
|
commitdiff
|
tree
2017-11-23
Berk Hess
Cor
r
ect PME GPU timin
g
nam
i
ng
commit
|
commitdiff
|
tree
2017-11-20
B
e
r
k
Hess
Preven
t
PME
tu
n
in
g
exces
s
ive
g
rid
s
c
a
l
i
n
g
commit
|
commitdiff
|
tree
2017-11-19
Be
r
k
Hes
s
A
dd SIMD
for AWH
commit
|
commitdiff
|
tree
2017-11-16
Berk Hess
Also print
1
x1 pair-list setup to log
commit
|
commitdiff
|
tree
2017-11-10
Berk Hess
Fix g
e
nion charge sum
m
ation
ac
c
uracy
commit
|
commitdiff
|
tree
2017-11-02
Berk Hess
Fix Ekin at step 0 with COM r
e
moval
commit
|
commitdiff
|
tree
2017-11-02
Be
r
k He
s
s
Add mis
s
ing Ewald correcti
o
n fo
r
pme-user
commit
|
commitdiff
|
tree
2017-10-30
Be
r
k Hes
s
Remove un
u
sed sign parameter from dih_angle()
commit
|
commitdiff
|
tree
2017-10-29
Berk
Hess
Re
m
ove incorrect comment
f
or CHARMM tip
s
3p
commit
|
commitdiff
|
tree
2017-10-24
B
e
rk Hess
F
i
x gmx ch
e
ck for tprs with differe
n
t #atoms
commit
|
commitdiff
|
tree
2017-10-23
Berk Hess
F
ix incorrect
d
V/d
l
ambd
a
for walls
commit
|
commitdiff
|
tree
2017-10-21
Berk Hess
M
erg
e
"
M
e
rge branch release-2016"
commit
|
commitdiff
|
tree
2017-10-20
Berk Hess
Fix
w
a
rning f
o
r conf
o
ut w
i
t
h
per
i
odic m
o
lecule
s
commit
|
commitdiff
|
tree
2017-10-18
Berk Hess
Made CUDA PME text
u
r
e
refere
n
ce con
d
itional
commit
|
commitdiff
|
tree
2017-10-15
Be
r
k Hess
Improve vsi
t
e
par
a
llel checki
n
g
commit
|
commitdiff
|
tree
2017-10-12
Berk H
e
ss
Sim
p
lify virial handling
commit
|
commitdiff
|
tree
2017-10-11
B
e
rk Hess
Dis
a
ble AR
M
Neon native rsqrt i
t
eration
commit
|
commitdiff
|
tree
2017-10-06
Ber
k
Hess
A
d
d accelera
t
ion correcti
o
n VCM mode
commit
|
commitdiff
|
tree
2017-10-06
Berk Hess
Fix max_size() in allo
c
ator
.
h
commit
|
commitdiff
|
tree
2017-10-06
Be
r
k
Hess
A
dd SIMD in
t
rinsic
s
version of si
m
ple up
d
ate
commit
|
commitdiff
|
tree
2017-10-06
Berk He
s
s
I
mprove P
a
dded
R
VecVector resizing
commit
|
commitdiff
|
tree
next