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Remove ineffective code for writing more TER fields to pdb files
2019-03-07
Mark
Abra
h
am
Remove i
n
ef
f
ecti
v
e cod
e
for wr
i
tin
g
more TER fields
.
.
.
commit
|
commitdiff
|
tree
2019-03-06
Mar
k
A
bra
h
am
Cl
e
an up
use of loop indices
commit
|
commitdiff
|
tree
2019-03-06
Berk Hess
Clean
up n
b
n
x
m bound
i
ng
box functio
n
s
commit
|
commitdiff
|
tree
2019-03-06
Be
r
k Hess
Clean up nbn
x
m bound
i
ng boxes
commit
|
commitdiff
|
tree
2019-03-06
Berk Hess
Convert nb
n
xm bounding
box
to a struct
commit
|
commitdiff
|
tree
2019-03-06
Mark Abr
a
ham
Revert "Eliminate
mdlib/mdrun
.
h
"
commit
|
commitdiff
|
tree
2019-03-06
Mark A
b
raham
Eli
m
inate
mdlib/mdrun
.
h
commit
|
commitdiff
|
tree
2019-03-06
Ma
r
k
Abra
h
a
m
Mi
n
or modernization in gmx_du
m
p
commit
|
commitdiff
|
tree
2019-03-05
Berk Hess
T
urn
nbnxn
_
grid_t into a class
commit
|
commitdiff
|
tree
2019-03-02
S
z
ilá
r
d Páll
Enc
a
p
sul
a
te force output setup in do_for
c
e_*
commit
|
commitdiff
|
tree
2019-03-02
M
a
rk Ab
r
aham
Merge branch release-20
1
9
commit
|
commitdiff
|
tree
2019-03-02
Mark
A
braham
Remove defunc
t
mdrun
o
ptions
commit
|
commitdiff
|
tree
2019-02-27
Jukka Maatta
Make OpenCL d
u
mmy
K
ernel to require a input
p
a
rameter
commit
|
commitdiff
|
tree
2019-02-26
Ma
r
k Abraham
Add n
e
w line to trjc
o
nv
n
o
tice t
o
users
commit
|
commitdiff
|
tree
2019-02-25
Prash
a
n
t
h Kand
u
ri
Movin
g
do_pbc_mt
o
p(
.
.
.
) functions to pbc
u
t
ils f
r
om
.
.
.
commit
|
commitdiff
|
tree
2019-02-25
Paul Bauer
Refact
o
r Exclus
i
onBlocks
commit
|
commitdiff
|
tree
2019-02-25
M
a
rk Abraham
De-duplicate gmx_tm
p
nam
and gmx_fop
e
n
_
temporary
commit
|
commitdiff
|
tree
2019-02-23
B
erk Hess
Move a
l
l nbnxm pruning
details into module
commit
|
commitdiff
|
tree
2019-02-23
Berk Hess
Hi
d
e inte
r
nals of nbnxm parlist
commit
|
commitdiff
|
tree
2019-02-22
Paul Bauer
A
d
d tests fo
r
ExclusionBl
o
cks
commit
|
commitdiff
|
tree
2019-02-21
Paul Bauer
Reorganize release not
e
s
commit
|
commitdiff
|
tree
2019-02-21
Berk Hess
Minor n
b
nxm
c
le
a
n
up
commit
|
commitdiff
|
tree
2019-02-21
B
e
rk
H
ess
Clean up nbnxm enums
commit
|
commitdiff
|
tree
2019-02-21
Artem Z
h
murov
T
est for LI
N
CS and SHAKE con
s
t
r
aints
.
commit
|
commitdiff
|
tree
2019-02-21
B
erk He
s
s
S
implif
y
m
a
ke
_
pairlist() call
s
ig
n
ature
commit
|
commitdiff
|
tree
2019-02-20
Pa
u
l Bauer
Fix release notes
for
m
at
t
i
ng
commit
|
commitdiff
|
tree
2019-02-17
Sz
i
lá
r
d P
á
l
l
Im
p
rove
GPU target co
m
pa
t
ib
i
lity error message
commit
|
commitdiff
|
tree
2019-02-17
Berk Hess
Use en
u
m class for nbnxm loca
l
i
t
y
commit
|
commitdiff
|
tree
2019-02-17
Berk Hess
Extract nbnxm grid
.
h
a
nd pa
i
rlistwork
.
h
commit
|
commitdiff
|
tree
2019-02-17
Be
r
k Hess
Fix compile
r
warn
i
ng
s
commit
|
commitdiff
|
tree
2019-02-17
Berk Hess
Move nbnxm
d
etails from sim_util
.
cpp
t
o
modu
l
e
commit
|
commitdiff
|
tree
2019-02-16
Berk
Hess
M
o
ve nbnxn fil
e
s
to nb
n
x
m directory
commit
|
commitdiff
|
tree
2019-02-15
Sz
i
l
ár
d
Pál
l
Extend GpuEventSynchron
i
zer to allow
on-device
s
ync
commit
|
commitdiff
|
tree
2019-02-15
S
e
m
en Ye
s
ylevskyy
F
ix
e
d misl
e
ading w
o
rding for m
e
mb
e
d
o
pti
o
n
.
commit
|
commitdiff
|
tree
2019-02-15
Seme
n
Yes
y
levskyy
A
d
d
n
ew sugg
e
s
t
ed external trajectory analysis tool
commit
|
commitdiff
|
tree
2019-02-15
Paul Bauer
Fix memory issu
e
s in
pre
p
rocess
commit
|
commitdiff
|
tree
2019-02-15
Pa
u
l Bauer
R
e
fa
c
tor vsi
t
e topol
o
gy
commit
|
commitdiff
|
tree
2019-02-15
Pa
u
l
B
auer
Fix tune_pme
commit
|
commitdiff
|
tree
2019-02-13
Mark Abraham
Improved electric-field
d
ocs
commit
|
commitdiff
|
tree
2019-02-13
Szilárd Páll
Disable instruction
f
usion on
P
ower8
commit
|
commitdiff
|
tree
2019-02-13
M
ark Ab
r
aham
Reduce coupli
n
g to padde
d
vec
t
or
.
h
commit
|
commitdiff
|
tree
2019-02-13
Paul Bau
e
r
Move sim
u
lat
e
d tempering default setting
commit
|
commitdiff
|
tree
2019-02-12
Mark Abraham
Quiet cl
a
ng warning
commit
|
commitdiff
|
tree
2019-02-12
Paul Bau
e
r
Refactor t_restp
commit
|
commitdiff
|
tree
2019-02-11
C
hristian Blau
view on Mul
t
i
D
im
A
rray
commit
|
commitdiff
|
tree
2019-02-11
Paul Bauer
Re
f
actor
t
_hack to M
o
leculePatc
h
es
commit
|
commitdiff
|
tree
2019-02-11
Paul Bau
e
r
Fix bu
g
in residue ty
p
e
re
a
din
g
commit
|
commitdiff
|
tree
2019-02-09
Berk He
s
s
Disallow r
e
run
with perturbed masses
or cons
t
raints
commit
|
commitdiff
|
tree
2019-02-08
M
a
rk
A
braham
Fix Intel co
m
piler warning
commit
|
commitdiff
|
tree
2019-02-08
David
van
d
e
r
S
p
oel
Increase tolerance
in Angle test
.
commit
|
commitdiff
|
tree
2019-02-08
Th
o
mas U
l
lmann
separated
.
rst documentation of
d
i
hedral PCA a
n
d hydroge
n
.
.
.
commit
|
commitdiff
|
tree
2019-02-07
Christian Blau
mdspan - add bracket operato
r
slicing
commit
|
commitdiff
|
tree
2019-02-07
R
o
l
and Schulz
Re
v
er
t
size to be unsign
e
d for Arr
a
y
R
e
f
commit
|
commitdiff
|
tree
2019-02-06
Paul Bauer
Refactor t_hackbloc
k
commit
|
commitdiff
|
tree
2019-02-06
Berk
Hes
s
F
i
x
s
egfault with
EM, DD
and
g
rou
p
s
c
h
eme
commit
|
commitdiff
|
tree
2019-02-04
R
o
land Schulz
Renam
e
all
s
ource files f
r
om
-
to _ for cons
i
stency
.
commit
|
commitdiff
|
tree
2019-02-04
Roland
S
chu
l
z
Fix cma
k
e policy warning
commit
|
commitdiff
|
tree
2019-01-30
Mark Ab
r
aham
Merge remote
b
r
a
nch
r
eleas
e
-2018 into release-2019
commit
|
commitdiff
|
tree
2019-01-30
Ma
r
k
A
br
a
ham
F
i
x r
e
lea
s
e notes i
s
sue links
commit
|
commitdiff
|
tree
2019-01-30
Mark Abraha
m
Fix release notes is
s
ue links
commit
|
commitdiff
|
tree
2019-01-28
R
o
land
S
c
hu
l
z
R
e
solve
C+
+
14 TODOs
commit
|
commitdiff
|
tree
2019-01-28
Mar
k
Abr
a
ham
Stop trying
t
o check nvcc
o
n
Windows
commit
|
commitdiff
|
tree
2019-01-28
Mark Abraham
B
u
mp CUDA req
u
irement to
9
.
0
commit
|
commitdiff
|
tree
2019-01-26
Roland
S
chulz
Fix clang warn
i
ng
commit
|
commitdiff
|
tree
2019-01-25
Roland S
c
hulz
Req
u
ire C++14
commit
|
commitdiff
|
tree
2019-01-25
Mar
k
Abra
h
am
Re
q
uire clang
3
.
6
commit
|
commitdiff
|
tree
2019-01-25
Mark A
b
raham
Fix po
s
t-submit build
commit
|
commitdiff
|
tree
2019-01-25
M
a
rk Abra
h
am
Bu
m
p required gcc compiler to 5
.
1
commit
|
commitdiff
|
tree
2019-01-25
Mark Abraham
Use native cma
k
e C++11 su
p
port
commit
|
commitdiff
|
tree
2019-01-24
P
a
ul Bauer
C
hange gcov
t
o
run on bs-
m
ic
commit
|
commitdiff
|
tree
2019-01-24
P
a
ul Baue
r
Change gc
o
v to
r
un on
b
s
-
mic
commit
|
commitdiff
|
tree
2019-01-23
Roland
Schulz
Rename gmx Variant
t
o
Any
commit
|
commitdiff
|
tree
2019-01-23
Christi
a
n Blau
M
u
lti
d
ime
n
sional data in
c
an
o
n
ical layout
.
commit
|
commitdiff
|
tree
2019-01-23
P
a
ul Bauer
I
n
troduce s
t
r
i
ng comparis
o
n functio
n
commit
|
commitdiff
|
tree
2019-01-22
Berk
H
ess
Add utili
t
y met
h
od to N
b
nxnP
a
i
rlistGp
u
commit
|
commitdiff
|
tree
2019-01-22
Berk Hess
R
emove no
w
usused GPU al
l
oc/free functions
commit
|
commitdiff
|
tree
2019-01-22
B
e
rk Hess
Convert NbnxnPairlistG
p
u
t
o C++
commit
|
commitdiff
|
tree
2019-01-22
Mark
Abraham
Remove in
i
t_m
d
and
i
mpr
o
ve init_em
commit
|
commitdiff
|
tree
2019-01-22
Chr
i
sto
p
h Ju
n
gh
a
n
s
gmxManageLmfit
.
cmake: enforce
u
s
ag
e
o
f 7
.
0
commit
|
commitdiff
|
tree
2019-01-21
Szilárd
Pá
l
l
Add CUDA
C
C 7
.
5 (Turing) s
u
ppor
t
with
nvcc
commit
|
commitdiff
|
tree
2019-01-21
B
e
rk
He
s
s
Conver
t
nbnxn
_
atomda
t
a
_
t
to C++
commit
|
commitdiff
|
tree
2019-01-21
Pau
l
Bauer
Refactor ResidueTypes
commit
|
commitdiff
|
tree
2019-01-18
Paul Bauer
Change one g
m
x_mtop_t atom loop to C++
commit
|
commitdiff
|
tree
2019-01-18
Mark Abraham
Remove ctest
s
ection called simple
commit
|
commitdiff
|
tree
2019-01-18
M
.
Eric Irrga
n
g
Remove
.
travi
s
.
y
m
l
Travis
-
C
I
co
n
fig fi
l
e
.
commit
|
commitdiff
|
tree
2019-01-17
Paul Baue
r
C
h
a
ng
e
ResidueTypes
to
c
lass
commit
|
commitdiff
|
tree
2019-01-16
Ma
r
k Abraham
Migrate test configura
t
i
o
n
o
ff bs_mac
commit
|
commitdiff
|
tree
2019-01-16
Mark Abr
a
ham
Remove
several unnecessary things
commit
|
commitdiff
|
tree
2019-01-16
Berk
H
e
ss
Rename Ho
s
tVector
t
o Padded
H
ostVector
commit
|
commitdiff
|
tree
2019-01-15
Mar
k
Abraham
R
everted standard ExternalPro
j
ect for FFTW down
l
oad
commit
|
commitdiff
|
tree
2019-01-15
Roland Schu
l
z
Req
u
ir
e
cmake 3
.
9
.
6
commit
|
commitdiff
|
tree
2019-01-15
Paul Bauer
Rem
o
ve raw pointers i
n
index
h
a
n
d
ling
commit
|
commitdiff
|
tree
2019-01-14
K
evin Boyd
Partial convers
i
on
of gmx
m
sd to std::
v
ecto
r
commit
|
commitdiff
|
tree
2019-01-14
Paul
B
auer
Refactor
AtomPrope
r
ties into C++
commit
|
commitdiff
|
tree
2019-01-13
Kevin Boyd
Add grompp chec
k
for usage of
"
define" f
i
eld in
mdp
commit
|
commitdiff
|
tree
2019-01-11
Paul Bau
e
r
Make AtomProperties class
with Impl
commit
|
commitdiff
|
tree
2019-01-11
Mark
Abraham
U
s
e
enu
m
cla
s
s
for
grompp directives
commit
|
commitdiff
|
tree
2019-01-11
Mark Abr
a
ham
F
ix typo in release notes
commit
|
commitdiff
|
tree
2019-01-11
Mark Abraham
Add help
e
r f
u
nctionality for
s
a
f
er enumerations
commit
|
commitdiff
|
tree
2019-01-11
D
avid van
d
er Spoel
Added low-leve
l
tes
t
s for improper d
i
hedrals
.
commit
|
commitdiff
|
tree
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