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Replace C-style library file handling with RAII approaches
2018-09-11
Mark Ab
r
aham
R
eplace C-
s
tyl
e
l
i
b
r
ary file h
a
nd
l
ing with
R
AII
approaches
commit
|
commitdiff
|
tree
2018-09-11
Ma
r
k A
b
ra
h
am
Impro
v
e DD logging
commit
|
commitdiff
|
tree
2018-09-11
Rolan
d
Schulz
Comp
i
le nonbonded kern
e
ls as C++
commit
|
commitdiff
|
tree
2018-09-11
David van der Spoel
A
dded option to gmx n
m
e
i
g to print ZPE
.
commit
|
commitdiff
|
tree
2018-09-11
Mark A
b
raham
Re
p
lace
re
a
dCo
n
f
o
rmation wi
t
h To
p
ologyInforma
t
ion
commit
|
commitdiff
|
tree
2018-09-11
Pascal Merz
Added trivial co
n
s
t qualifiers
commit
|
commitdiff
|
tree
2018-09-11
Pascal Merz
Initialize
total
_
vi
r
and pres
in in
i
t_m
d
commit
|
commitdiff
|
tree
2018-09-10
Roland
Schulz
Replace rounding using int(x+0
.
5) with roun
d
ToInt
commit
|
commitdiff
|
tree
2018-09-10
R
ol
a
nd Sch
u
lz
Add roundToI
n
t
commit
|
commitdiff
|
tree
2018-09-09
Mark Abrah
a
m
Change Topol
o
gyInforma
t
ion implementation
commit
|
commitdiff
|
tree
2018-09-09
Paul B
a
u
e
r
Remove macr
o
for group type in topology
commit
|
commitdiff
|
tree
2018-09-07
M
ark Abraham
Fix gromp
p
me
m
ory lea
k
s
commit
|
commitdiff
|
tree
2018-09-07
Roland S
c
hulz
c
lang-tidy: override
commit
|
commitdiff
|
tree
2018-09-07
Magnus L
u
ndborg
C
h
e
ck q
pe
r
tu
r
ba
t
ion when PM
E
on GPU
is tested
commit
|
commitdiff
|
tree
2018-09-06
Roland Schulz
HostAllocator: Remov
e
un
n
ecessa
r
y template
commit
|
commitdiff
|
tree
2018-09-06
Roland Schul
z
R
emove pin/unpi
n
from HostA
l
l
ocato
r
commit
|
commitdiff
|
tree
2018-09-05
Paul Bauer
C
ha
n
ges
to d
o
cu
m
e
nt
a
ti
o
n b
u
ild scri
p
t
commit
|
commitdiff
|
tree
2018-08-30
P
aul Bauer
Mor
e
fixes fr
o
m cl
a
ng-tidy-7
commit
|
commitdiff
|
tree
2018-08-30
Ch
r
istian Bl
a
u
Store essential dynamics p
a
rameters as vecto
r
s ins
t
ead
.
.
.
commit
|
commitdiff
|
tree
2018-08-30
M
ark Abraham
Update testing
m
a
tr
i
c
es f
o
r
coverage
and speed
commit
|
commitdiff
|
tree
2018-08-29
M
a
r
k
Abraham
Merg
e
br
a
nch release-
2
0
18
commit
|
commitdiff
|
tree
2018-08-29
Berk Hess
Refactor
wall po
t
ential
calculation
commit
|
commitdiff
|
tree
2018-08-29
Ro
l
and Schulz
Use more const in h
a
rdwaretopology
commit
|
commitdiff
|
tree
2018-08-29
R
o
land Schulz
Fix cl
a
ng-tidy b
u
ild wit
h
libst
d
c++ >= 7
commit
|
commitdiff
|
tree
2018-08-29
Mar
k
A
b
raha
m
M
ove
c
l
ang-tidy bu
i
ld
commit
|
commitdiff
|
tree
2018-08-28
Mark Abraha
m
Fix more clang-ti
d
y issu
e
s
commit
|
commitdiff
|
tree
2018-08-28
Szilárd Páll
Quiet cma
k
e about clFFT n
o
t found after firs
t
run
commit
|
commitdiff
|
tree
2018-08-28
bori
s
tim
Updates to gmx clust
e
r
commit
|
commitdiff
|
tree
2018-08-28
Ro
l
and
Schul
z
Add har
d
limit for
line le
n
gth
commit
|
commitdiff
|
tree
2018-08-27
Mark Abraham
Fix
use of nullptr
commit
|
commitdiff
|
tree
2018-08-27
P
aul Bauer
Transfer informatio
n
fr
o
m old how-to section
commit
|
commitdiff
|
tree
2018-08-27
Rola
n
d Schulz
E
n
able more cl
a
ng-tidy
c
hecks for ne
w
code
commit
|
commitdiff
|
tree
2018-08-24
Mark Abraham
Fi
x
build without TN
G
commit
|
commitdiff
|
tree
2018-08-24
Mark Abraham
Merge branch
r
e
lease-2018
commit
|
commitdiff
|
tree
2018-08-22
P
a
u
l Bauer
Fix
t
rjconv wh
e
n running witho
u
t a structure file
commit
|
commitdiff
|
tree
2018-08-22
Mark Abraham
Fix h
a
ndling of counter resets
commit
|
commitdiff
|
tree
2018-08-22
Joe Jordan
Fix pdb2gmx -chainsep
commit
|
commitdiff
|
tree
2018-08-21
Mark Abr
a
ham
Re-imp
l
emented mdrun -rerun
t
ests
commit
|
commitdiff
|
tree
2018-08-21
Ma
r
k Abraham
Fix assertions for SD update
commit
|
commitdiff
|
tree
2018-08-21
Christian Blau
Add test
for structural simi
l
arity
mea
s
ure
s
rm
s
d
a
nd
.
.
.
commit
|
commitdiff
|
tree
2018-08-20
Berk Hess
Re
f
a
c
tor calc_verle
t
_buffe
r
_size()
commit
|
commitdiff
|
tree
2018-08-20
S
z
ilárd Páll
D
isable single c
o
mpilation unit wit
h
CUDA 9
.
0
commit
|
commitdiff
|
tree
2018-08-20
Berk Hes
s
Fix Verlet buffer estima
t
e with BD
commit
|
commitdiff
|
tree
2018-08-20
Berk Hess
Fi
x
a
s
se
r
t
ion
f
ailure
i
n CG
commit
|
commitdiff
|
tree
2018-08-20
Berk Hess
R
eally fi
x
CG with mu
l
t
i
p
l
e d
o
mains
commit
|
commitdiff
|
tree
2018-08-19
R
o
l
and S
c
h
ul
z
Fix simd-tes
t
commit
|
commitdiff
|
tree
2018-08-18
Roland S
c
hulz
readability-implicit-bool-conversion 2
/
2
commit
|
commitdiff
|
tree
2018-08-18
Roland Sch
u
lz
Enable cla
n
g t
i
dy
/
warnings
f
or
te
s
ts
commit
|
commitdiff
|
tree
2018-08-14
Paul
B
a
u
er
Updated
l
inks in user g
u
ide
commit
|
commitdiff
|
tree
2018-08-14
R
oland S
c
hulz
F
ix int/bool b
u
gs
commit
|
commitdiff
|
tree
2018-08-14
Joe Jordan
Add
c
hainsep and merge test
s
f
o
r
pdb2gmx
commit
|
commitdiff
|
tree
2018-08-14
Mark Abraham
Fi
x
enforced rotation energy o
u
tput
commit
|
commitdiff
|
tree
2018-08-12
Roland Schu
l
z
Add
_real user defined literal
commit
|
commitdiff
|
tree
2018-08-08
C
hristian Blau
Local atom
s
et
s
in rotatio
n
al pulling
.
commit
|
commitdiff
|
tree
2018-08-08
Ro
l
and Schu
l
z
2/3
o
f old-style casting
commit
|
commitdiff
|
tree
2018-08-07
Pau
l
B
auer
R
e
move
d
uplicate
e
ntry for Doxygen from de
v
ma
n
ual
commit
|
commitdiff
|
tree
2018-08-07
Chris
t
ian Bl
a
u
Local
at
o
m sets in com
p
EL / ion swa
p
ping cod
e
.
commit
|
commitdiff
|
tree
2018-08-07
Roland Schulz
Fix clang-tidy MPI warning
s
commit
|
commitdiff
|
tree
2018-08-06
R
o
l
and Schulz
Chan
g
e gmx_bool from
int to bool
commit
|
commitdiff
|
tree
2018-08-06
R
olan
d
Schulz
Disa
b
le F
P
E for GCC
7
.
* with optimizations
commit
|
commitdiff
|
tree
2018-08-05
Mark
A
b
r
aham
Reform e
n
forced rotation work
i
ng
d
a
ta
commit
|
commitdiff
|
tree
2018-08-04
Roland Schulz
clang-tidy: m
o
dernize make
-
uniqu
e
/shared
commit
|
commitdiff
|
tree
2018-08-04
Christian Bla
u
Sp
l
it essential dynamics
r
eading routine
commit
|
commitdiff
|
tree
2018-08-01
M
.
Eri
c
Irrgang
Remo
v
e extran
e
o
u
s gitign
o
re li
n
e
.
commit
|
commitdiff
|
tree
2018-07-31
Mark Abraham
Clean
u
p inputre
c
st
r
uct
s
commit
|
commitdiff
|
tree
2018-07-30
Szil
á
rd Páll
Move out OpenCL d
e
vice utils from v
e
ctype
ops
commit
|
commitdiff
|
tree
2018-07-30
Aleksei Iu
p
inov
Remove hardcoded warp_si
z
e ==
3
2 assumption
f
rom PME
G
PU
commit
|
commitdiff
|
tree
2018-07-30
M
a
rk
A
b
r
a
h
a
m
Fix CG
w
ith multiple d
o
main
s
commit
|
commitdiff
|
tree
2018-07-30
Roland Schulz
Disable FPE
s
at end of run
n
er
commit
|
commitdiff
|
tree
2018-07-30
Paul Bauer
Fix bfactor output
commit
|
commitdiff
|
tree
2018-07-29
Szilárd Páll
Corre
c
tions to the user guid
e
mdrun perf sect
i
o
n
commit
|
commitdiff
|
tree
2018-07-18
Berk
Hess
Apply local atom
se
t
s in pu
l
l code
commit
|
commitdiff
|
tree
2018-07-18
Mark Abraham
F
i
x pre-submit ma
t
rix
commit
|
commitdiff
|
tree
2018-07-17
Mark
A
braham
Update clan
g
static a
n
alyzer to
v
ersion 6
commit
|
commitdiff
|
tree
2018-07-17
Joe Jordan
change gmx_bool t
o
bool in gmxpre
p
rocess
commit
|
commitdiff
|
tree
2018-07-17
Christian Blau
L
ocal atom
se
t
hand
l
ing during simulat
i
ons
.
commit
|
commitdiff
|
tree
2018-07-16
Rolan
d
Schulz
Fix Windows+Intel
commit
|
commitdiff
|
tree
2018-07-16
Christian
Blau
Add LocalAto
m
Set for hand
l
i
ng atom in
d
ices
.
commit
|
commitdiff
|
tree
2018-07-16
Mark Abraham
Upda
t
ed infr
a
s
t
ru
c
t
u
re f
o
r comparing
m
drun output in
.
.
.
commit
|
commitdiff
|
tree
2018-07-16
Roland Schulz
Warn fo
r
typ
e
mismatch f
o
r
g
mx p
r
intf
like fu
n
c
tions 1/3
commit
|
commitdiff
|
tree
2018-07-16
M
a
rk
Abrah
a
m
Replacem
e
nt
for pdb
2
gmx
te
s
ts
commit
|
commitdiff
|
tree
2018-07-16
Rol
a
nd Schulz
Enab
l
e deb
u
g FP
e
xcept
i
ons without TPI, n
o
t w
i
th
TP
I
commit
|
commitdiff
|
tree
2018-07-12
Ro
l
a
nd
Sc
h
ulz
Fix
a
ttrib
u
te usag
e
commit
|
commitdiff
|
tree
2018-07-11
Roland Sch
u
lz
c
l
ang: unde
f
ine
d
-
reinterpr
e
t
-ca
s
t, com
m
a, extra-semi
commit
|
commitdiff
|
tree
2018-07-11
Roland Schulz
Fix cust
o
m build types with
c
make 3
.
11
commit
|
commitdiff
|
tree
2018-07-11
Roland Sc
h
u
l
z
Clang warn
i
n
gs
commit
|
commitdiff
|
tree
2018-07-11
Mark
A
br
a
ham
S
plit Topolog
y
Infor
m
atio
n
i
n
t
o
i
t
s own
h
eader
commit
|
commitdiff
|
tree
2018-07-08
Mark
Abraham
Cla
r
ify the implem
e
ntation o
f
selection -ofp
d
b output
commit
|
commitdiff
|
tree
2018-07-06
Mark
A
braham
Fix warnings in internal
x
d
r
code
commit
|
commitdiff
|
tree
2018-07-06
Mark Abraham
Merge "Me
r
ge rel
e
ase
-
2
0
18 in
t
o master
"
commit
|
commitdiff
|
tree
2018-07-06
Rolan
d
Schulz
F
ix AVX_512_KNL
commit
|
commitdiff
|
tree
2018-07-04
Roland Schul
z
Fix ManageLmfit
commit
|
commitdiff
|
tree
2018-07-03
Rol
a
nd S
c
hulz
Ch
a
nge ArrayRef::size_type t
o
signed
commit
|
commitdiff
|
tree
2018-07-03
B
e
rk Hess
Convert
g
mx_hash
_
t to C++
commit
|
commitdiff
|
tree
2018-07-03
Roland Schulz
clang-tidy: misc-misplaced-widening-
c
ast
commit
|
commitdiff
|
tree
2018-07-03
Roland Sch
u
lz
clang-t
i
dy: misc-mispl
a
ced-co
n
st
commit
|
commitdiff
|
tree
2018-07-03
Berk
H
ess
Localize va
r
iables in dd_r
e
distribu
t
e_cg()
commit
|
commitdiff
|
tree
2018-07-02
Ber
k
Hess
Con
v
ert DD
D
LB
c
ell
s
ize hand
l
ing to
C
++
commit
|
commitdiff
|
tree
2018-07-01
R
o
land Schulz
E
n
able clang-tidy N
u
llDere
f
eren
c
e
commit
|
commitdiff
|
tree
2018-07-01
R
o
l
a
nd Schulz
cla
n
g-tidy: readability-non-cons
t
-param
e
ter (2/
2
)
commit
|
commitdiff
|
tree
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