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Fix warnings with clang 9
2020-04-17
P
a
scal Merz
Mak
e
global
t
opology const in ISi
m
u
l
a
tor
commit
|
commitdiff
|
tree
2020-04-14
P
a
scal Merz
Ma
k
e
bo
n
de
d
int
e
rac
t
ion checking mo
r
e robus
t
(modula
r
.
.
.
commit
|
commitdiff
|
tree
2020-04-07
Pas
c
al Merz
Merge fo
r
c
e a
n
d shellFC elements
commit
|
commitdiff
|
tree
2020-04-07
Pasca
l
Merz
Requ
i
r
e
explicit MPI_COMM f
o
r gmx_
b
cast and gmx_barrier
commit
|
commitdiff
|
tree
2020-04-07
P
a
scal Mer
z
Make global
topol
o
g
y
constant in energyOutp
u
t
.
pri
n
tAnnea
l
ing
.
.
.
commit
|
commitdiff
|
tree
2020-04-07
Pascal Me
r
z
Mak
e
global topology const in minimization
commit
|
commitdiff
|
tree
2020-04-06
Pascal
Merz
Ma
k
e global topology constant in mdoutf
commit
|
commitdiff
|
tree
2020-04-06
Pascal Mer
z
Make bonded in
t
e
racti
o
n ch
e
cking more robus
t
(modul
a
r
.
.
.
commit
|
commitdiff
|
tree
2020-02-27
P
ascal M
e
rz
Loosen
gmxapi stopsignaler
t
est
commit
|
commitdiff
|
tree
2020-02-27
Pascal Merz
Us
e
legacy code path for t_graph (modular simulator)
commit
|
commitdiff
|
tree
2020-02-27
Pascal Merz
Extra
c
t and ex
p
ose function to de
t
ermine wheth
e
r molecules
.
.
.
commit
|
commitdiff
|
tree
2020-02-26
Pascal Merz
Fi
x
c
o
nstraint contribution to dhdl (modula
r
s
imulator)
commit
|
commitdiff
|
tree
2020-02-26
Pas
c
al Merz
Fix calculation of reciprocal terms
in rer
u
n
commit
|
commitdiff
|
tree
2020-02-24
Pascal Merz
U
s
e
ArrayRef
i
n compute_globals
commit
|
commitdiff
|
tree
2020-02-21
Pas
c
al Mer
z
Use
legacy code pa
t
h for NMR restr
a
ints (
m
odular
s
i
m
u
l
ator)
commit
|
commitdiff
|
tree
2020-02-21
P
a
sca
l
Merz
C
o
rrect for skewed box in
non
-
DD modul
a
r si
m
u
l
a
tor
commit
|
commitdiff
|
tree
2020-02-14
Pascal Merz
Expa
n
d test coverage of exac
t
c
ontin
u
ation tests
commit
|
commitdiff
|
tree
2020-02-14
P
a
s
c
al
Merz
Fix reading of checkpoints with Parr
i
nello-Rahman
.
.
.
commit
|
commitdiff
|
tree
2020-02-14
Pascal Merz
Fix Parrinello-Rah
m
an scaling on initi
a
l step (m
o
dula
r
.
.
.
commit
|
commitdiff
|
tree
2020-02-14
Pascal Merz
Move mod
u
lar s
i
mulator decision bef
o
re
c
he
c
kpoint loading
commit
|
commitdiff
|
tree
2020-02-13
Pas
c
al Merz
Fix c
h
e
c
kNumberOfBondedI
n
teractions bug
commit
|
commitdiff
|
tree
2020-02-13
Pas
c
a
l Merz
E
x
pose vs
i
t
e
counting
commit
|
commitdiff
|
tree
2020-02-05
Pascal Merz
Te
s
t Pa
d
dedV
e
ctor to Arr
a
yRef conve
r
sion
commit
|
commitdiff
|
tree
2020-02-05
Pasc
a
l Mer
z
Minor imp
r
ov
e
ment
s
to
vcm
.
cpp
commit
|
commitdiff
|
tree
2020-02-05
Pascal Merz
Merge
V
V implementations of Com
p
uteGlobalsEl
e
ment
commit
|
commitdiff
|
tree
2020-01-31
Pascal Mer
z
Modul
a
r simulator: Al
l
ow for nullptr in
e
lement list
.
.
.
commit
|
commitdiff
|
tree
2020-01-31
P
a
scal Me
r
z
S
t
atePropagatorData: M
a
ke const box ge
t
ter
s
cons
t
funct
i
ons
commit
|
commitdiff
|
tree
2020-01-31
Pascal Merz
M
ake
t
_
inputrec
c
onst i
n
C
om
p
uteGlob
a
l
s
Element
commit
|
commitdiff
|
tree
2019-12-17
P
asca
l
Merz
F
i
x ex
a
ct conti
n
uation
modular simulato
r
commit
|
commitdiff
|
tree
2019-12-12
Pasc
a
l
M
erz
Te
s
t
for
expected
outpu
t
f
iles
commit
|
commitdiff
|
tree
2019-12-12
P
a
sca
l
Merz
Fi
x
fi
n
a
l configuration writin
g
for
m
odular simulator
commit
|
commitdiff
|
tree
2019-10-31
Pascal
M
e
rz
Check for contrad
i
cting environment
v
a
r
i
ab
l
es (modular
.
.
.
commit
|
commitdiff
|
tree
2019-10-30
Pascal Merz
Fix doxyge
n
for modular simulator
commit
|
commitdiff
|
tree
2019-10-30
P
ascal Mer
z
Fix
m
odular simulator document
a
tion
commit
|
commitdiff
|
tree
2019-10-29
Pas
c
al Merz
Fix compa
t
ibili
t
y
c
heck of
m
odula
r
simulat
o
r
commit
|
commitdiff
|
tree
2019-10-27
Pasca
l
Merz
Enable
f
orced
r
otati
o
n for modular
simula
t
or
commit
|
commitdiff
|
tree
2019-10-23
P
a
s
c
al Merz
Co
r
rect f
o
r skewed b
o
x befor
e
domain deco
m
pos
i
ti
o
n
.
.
.
commit
|
commitdiff
|
tree
2019-10-23
Pascal M
e
rz
F
i
x log w
r
itin
g
(m
o
dular simulator)
commit
|
commitdiff
|
tree
2019-10-23
Pascal Merz
Adapt enum to st
y
le convention (modular si
m
ulator
)
commit
|
commitdiff
|
tree
2019-10-23
Pascal
M
e
rz
Sma
l
l imp
r
ovement to Energy
E
lement (modul
a
r simulator)
commit
|
commitdiff
|
tree
2019-10-22
Pascal Merz
Fix sto
p
condit
i
on handling (modu
l
a
r
s
i
mulator)
commit
|
commitdiff
|
tree
2019-10-22
Pascal Merz
Fix
sign
a
l propagation (m
o
d
u
lar simula
t
or)
commit
|
commitdiff
|
tree
2019-10-22
Pascal
M
e
r
z
Fix DomDec
s
tep (modular simulat
o
r)
commit
|
commitdiff
|
tree
2019-10-22
Pascal Mer
z
Fix PmeL
o
adBala
n
ceHelper
i
n
itia
l
ization
(
modular sim
u
lator)
commit
|
commitdiff
|
tree
2019-10-01
Pas
c
al Merz
Output correct kinetic at last step (modular simul
a
tor
)
commit
|
commitdiff
|
tree
2019-09-23
Pascal Merz
Parr
i
ne
l
l
o
-
Rah
m
an for md-vv
commit
|
commitdiff
|
tree
2019-09-23
P
a
s
cal Merz
Parrinello-Rahman barostat
f
or modular s
i
mulator (leap
.
.
.
commit
|
commitdiff
|
tree
2019-09-23
Pas
c
al Merz
Zero pr
e
ssure and virial tensor
s
a
t
beginning of
step
commit
|
commitdiff
|
tree
2019-09-23
Pascal
M
erz
Int
r
od
u
c
e FE
P
into modul
a
r simu
l
ator
commit
|
commitdiff
|
tree
2019-09-23
Pascal Merz
M
a
ke Che
c
kpointHel
p
er safer and eas
i
er to us
e
commit
|
commitdiff
|
tree
2019-09-23
P
a
scal Merz
Fix
v
resca
l
e thermostat
i
ntegra
l
(modular simulator)
commit
|
commitdiff
|
tree
2019-09-20
Pascal Merz
Fix rest
a
rts in
m
odul
a
r sim
u
l
ator
commit
|
commitdiff
|
tree
2019-09-20
Pascal
M
erz
Fix domdec for m
d
-vv modular simulator
commit
|
commitdiff
|
tree
2019-09-20
Pascal M
e
rz
Run simula
t
o
r equiva
l
ence t
e
sts in do
u
bl
e
precision
.
.
.
commit
|
commitdiff
|
tree
2019-09-18
Pa
s
cal Mer
z
v-resc
a
le thermostat for m
o
dul
a
r sim
u
lator
commit
|
commitdiff
|
tree
2019-09-17
Pascal
M
e
r
z
Mino
r
twe
a
ks t
o
sum_dhdl and setCurrentLambdasLoc
a
l
commit
|
commitdiff
|
tree
2019-09-17
Pasca
l
M
erz
Fix position pinn
i
ng for m
o
dular simulator
commit
|
commitdiff
|
tree
2019-09-17
Pascal Merz
Fix modular simulat
o
r MPI bugs
commit
|
commitdiff
|
tree
2019-09-17
Pascal
M
erz
M
a
ke mod
u
lar
si
m
u
lator the def
a
u
lt code p
a
th for md
.
.
.
commit
|
commitdiff
|
tree
2019-09-17
Pascal Merz
Fix force element
commit
|
commitdiff
|
tree
2019-09-17
Pascal Me
r
z
Enable checkpointing for modular
s
i
m
ulator
commit
|
commitdiff
|
tree
2019-09-15
Pas
c
a
l
Merz
Introduce th
e
modular
simulator
commit
|
commitdiff
|
tree
2019-09-12
P
asc
a
l
Merz
Up
d
a
te modular simulat
o
r te
s
ts
commit
|
commitdiff
|
tree
2019-09-10
Pascal M
e
rz
Comp
o
siteSimul
a
torElement
for the mod
u
la
r
s
imul
a
tor
commit
|
commitdiff
|
tree
2019-09-10
P
ascal
Merz
C
o
o
rdinate Propagator
s
commit
|
commitdiff
|
tree
2019-09-10
Pascal Merz
S
t
a
t
ePropagato
r
Data:
I
nt
r
oduced co
n
st box acces
s
or
.
.
.
commit
|
commitdiff
|
tree
2019-09-10
Pascal Merz
Ad
d
trivial co
n
s
t qualifier
s
to sh
e
ll
f
c
a
nd EnergyOutp
u
t
commit
|
commitdiff
|
tree
2019-09-10
P
a
scal
Merz
C
onstrain
t
el
e
ment for
t
he
m
o
d
ular simulator
commit
|
commitdiff
|
tree
2019-09-09
Pascal Merz
D
omain decom
p
o
s
i
tion and P
M
E l
o
ad balan
c
ing for modular
.
.
.
commit
|
commitdiff
|
tree
2019-09-07
P
ascal Merz
M
a
ke pme_loadbal_do() indepen
d
ent of t_state
commit
|
commitdiff
|
tree
2019-09-07
Pa
s
cal Merz
ForceEleme
n
t
and ShellFCElement for the modular
simulator
commit
|
commitdiff
|
tree
2019-09-06
Pa
s
cal Merz
Com
p
uteGl
o
ba
l
sElement for the
m
odular si
m
ulator
commit
|
commitdiff
|
tree
2019-09-05
Pascal Merz
Introduce topology class fo
r
modular simulator
commit
|
commitdiff
|
tree
2019-09-05
Pa
s
cal
M
erz
Ren
a
me
MicroState
t
o StatePropagatorData for modular
.
.
.
commit
|
commitdiff
|
tree
2019-09-05
Pas
c
a
l
M
erz
Ad
a
p
t
inheritance int
e
ndati
o
n
to un
c
ru
s
t
i
f
y
commit
|
commitdiff
|
tree
2019-09-05
Pascal Merz
M
a
k
e do_constrai
n
_first() i
n
dependent of t_sta
t
e
commit
|
commitdiff
|
tree
2019-09-03
Pascal Merz
Intr
o
duce energy element f
o
r modular si
m
ulato
r
commit
|
commitdiff
|
tree
2019-08-28
Pascal M
e
rz
Intro
d
u
c
e MicroS
t
ate for modular
s
imulator
commit
|
commitdiff
|
tree
2019-08-28
Pasca
l
M
erz
Intr
o
duce
signallers for
m
o
dular in
t
egrator
commit
|
commitdiff
|
tree
2019-08-28
Pascal Merz
Introduce the main mod
u
lar simu
l
at
o
r int
e
rfaces an
d
.
.
.
commit
|
commitdiff
|
tree
2019-08-12
Pascal Merz
Use new seten
v
functi
o
n for e
n
ergyo
u
t
put test
commit
|
commitdiff
|
tree
2019-08-05
Pascal
Merz
Add trivial
c
onst qualif
i
er to en
e
r
g
y output
commit
|
commitdiff
|
tree
2019-08-05
Pa
s
c
a
l Merz
Add const g
e
tter to MDAtoms
commit
|
commitdiff
|
tree
2019-08-05
P
ascal M
e
rz
M
ove ownership
o
f
kineti
c
energy object
to ISimulator
commit
|
commitdiff
|
tree
2019-08-05
Pascal Merz
Added S
i
mulato
r
comparison
test
commit
|
commitdiff
|
tree
2019-08-05
P
a
scal Merz
Introduce SimulatorBuilder
commit
|
commitdiff
|
tree
2019-08-02
Pascal
M
erz
I
ntroduce Simula
t
or base cla
s
s
commit
|
commitdiff
|
tree
2019-07-31
Pascal M
e
r
z
Rename Si
m
ulator to LegacyS
i
m
u
l
ator
commit
|
commitdiff
|
tree
2019-07-11
P
a
scal
Merz
Get ri
d
of clang-tidy warning in
d
o
_md/reru
n
/
m
i
mic
commit
|
commitdiff
|
tree
2019-07-11
Pascal Merz
Remove dependence of compute
_
g
l
o
b
als
o
n t_state
commit
|
commitdiff
|
tree
2019-07-11
P
ascal Merz
M
ake relax_shell_flexcon independent of t_state
commit
|
commitdiff
|
tree
2019-07-09
Pascal Merz
A
dded trivia
l
const qualifier to
r
elax_shel
l
_fle
x
con()
commit
|
commitdiff
|
tree
2019-07-09
Pascal Merz
Con
s
t qualifier for forces i
n
update_coords
commit
|
commitdiff
|
tree
2019-07-01
Pa
s
cal Merz
F
ix
module detection for physical validat
i
on
commit
|
commitdiff
|
tree
2019-06-24
Pascal Merz
Ma
k
e global topology constant in trajectory writing
commit
|
commitdiff
|
tree
2019-05-27
Pascal Merz
Clean up renamed sim
u
lator
.
h file
commit
|
commitdiff
|
tree
2019-05-25
Pascal Merz
R
e
move depe
n
dence
of mdoutf_write_to_tra
j
ectory_files
.
.
.
commit
|
commitdiff
|
tree
2019-05-25
Pascal Merz
R
ename Int
e
grator class
commit
|
commitdiff
|
tree
2019-05-16
Pas
c
al Merz
Use Pyt
h
on 3
commit
|
commitdiff
|
tree
2018-12-10
Pascal Merz
Failproof s
i
g
n
a
l conversion
commit
|
commitdiff
|
tree
next