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Separate job script files for gmxapi package versions.
2020-11-10
Pas
c
al Merz
Fi
x
MTTK
consta
n
t energy bug
s
commit
|
commitdiff
|
tree
2020-10-05
Pascal Merz
Fix ForceBuf
f
ers compiler
warning
commit
|
commitdiff
|
tree
2020-10-01
Pascal Merz
Update
m
odular simulator docs
commit
|
commitdiff
|
tree
2020-09-30
Pascal
Me
r
z
Regr
e
s
sio
n
-test-styl
e
Google tests for FEP
commit
|
commitdiff
|
tree
2020-09-30
P
a
scal
M
e
rz
Fix b
u
g rese
t
ting mdatoms ma
s
ses to
l
a
m
b
da=0 s
t
a
t
e
commit
|
commitdiff
|
tree
2020-09-30
P
ascal Merz
Fix #3
6
5
5
commit
|
commitdiff
|
tree
2020-09-30
Pascal Merz
Fix #3694
commit
|
commitdiff
|
tree
2020-09-29
Pascal Merz
Fix bug reset
t
ing mdatoms masses to lambda=0 state
commit
|
commitdiff
|
tree
2020-09-27
Pas
c
al
Merz
Compare trajec
t
ories to reference da
t
a
commit
|
commitdiff
|
tree
2020-09-27
Pas
c
al M
e
rz
Roll back "Ensure the modular s
i
mulator runs only when
.
.
.
commit
|
commitdiff
|
tree
2020-09-25
P
a
sca
l
Merz
R
eplace Fr
a
me
s
ToCompa
r
e enum by MaxNumF
r
ames
commit
|
commitdiff
|
tree
2020-09-23
Pas
c
al Merz
Acc
e
ss
write c
h
eckpoi
n
t
f
un
c
tionality directly
commit
|
commitdiff
|
tree
2020-09-23
Pascal Merz
Implement
Berendsen t
h
er
m
ostat for m
o
dular s
i
mulator
commit
|
commitdiff
|
tree
2020-09-21
Pascal
Mer
z
Checkpo
i
ntdata DD follow
u
p
commit
|
commitdiff
|
tree
2020-09-18
Pascal Merz
R
efactor v-r
e
s
c
a
le thermost
a
t to allow for other algorithms
commit
|
commitdiff
|
tree
2020-09-17
Pasc
a
l
Merz
Ren
a
me V
R
escaleThermostat to VelocityScal
i
ng
T
emperature
C
oup
l
ing
commit
|
commitdiff
|
tree
2020-09-16
Pascal M
e
rz
Implemen
t
modular ch
e
ck
p
ointing
commit
|
commitdiff
|
tree
2020-09-08
Pasc
a
l Merz
Mak
e
legacy energy
e
lements use CheckpointData
commit
|
commitdiff
|
tree
2020-09-08
P
a
scal M
e
rz
Remove dependen
c
y of EnergyData on t
_
state
commit
|
commitdiff
|
tree
2020-09-07
P
ascal Merz
Make EnergyOutput
:
:addDa
t
aAtEnergyStep independent
.
.
.
commit
|
commitdiff
|
tree
2020-09-06
Pasc
a
l Mer
z
Prepa
r
e l
e
gacy
checkpoin
t
for modu
l
ar s
i
mulator ch
e
ckpointing
commit
|
commitdiff
|
tree
2020-09-06
Pas
c
al Merz
M
o
dul
a
r
s
imulator:
Simplif
y
velocity updat
e
dispatch
commit
|
commitdiff
|
tree
2020-09-04
Pascal
M
e
rz
Intro
d
uce Checkpoi
n
tData
commit
|
commitdiff
|
tree
2020-09-03
Pascal Me
r
z
Re
m
ove unnecessary frie
n
d decl
a
ration
commit
|
commitdiff
|
tree
2020-09-03
Pas
c
al Merz
Mak
e
dd_col
l
ect_vec in
d
ep
e
ndent of
t
_state
commit
|
commitdiff
|
tree
2020-08-17
Pascal Merz
U
se proper
do
x
yge
n
t
a
g
s
in
modu
l
a
r
simulator
commit
|
commitdiff
|
tree
2020-08-16
Pascal
Me
r
z
Modu
l
a
r
simulator: Don't wr
a
p s
t
d::function in un
i
que_ptr
commit
|
commitdiff
|
tree
2020-08-14
Pascal Merz
I
ntroduce flexible M
o
dularSimul
a
torAlgorithm
B
ui
l
der
.
.
.
commit
|
commitdiff
|
tree
2020-08-07
Pascal Merz
I
n
troduc
e
GlobalCommunicati
o
n
H
elper
commit
|
commitdiff
|
tree
2020-08-07
Pasc
a
l Merz
Im
p
rove
m
o
d
ul
a
r
s
imulator builders
commit
|
commitdiff
|
tree
2020-08-07
P
a
scal Merz
Separate I
S
imulator i
n
terfa
c
e
a
nd data
commit
|
commitdiff
|
tree
2020-07-18
P
a
s
cal Me
r
z
Follow up to "Sep
a
ra
t
e State
P
r
opagator
D
ata element
.
.
.
commit
|
commitdiff
|
tree
2020-07-17
Pas
c
al Merz
Introduc
e
modular
s
imul
a
tor
excepti
o
ns
commit
|
commitdiff
|
tree
2020-07-15
Pascal M
e
rz
Se
p
arate Ele
m
ent f
r
om Fre
e
En
e
rgy
P
erturbationDa
t
a
commit
|
commitdiff
|
tree
2020-07-14
Pascal Merz
Se
p
arate en
e
rgy data a
n
d element
commit
|
commitdiff
|
tree
2020-07-09
Pascal Me
r
z
Divide defa
u
lt communicator from DD co
m
municators
commit
|
commitdiff
|
tree
2020-07-08
Pascal
Merz
S
e
parate StateP
r
o
p
agatorDa
t
a element
commit
|
commitdiff
|
tree
2020-07-07
Pascal
M
er
z
Anno
t
ate
modular simula
t
or
h
eaders wit
h
exposure level
commit
|
commitdiff
|
tree
2020-07-03
Pascal Merz
Sep
a
rate Mo
d
ularS
i
mulator
a
n
d ModularSimul
a
torAlg
o
ri
t
hm
commit
|
commitdiff
|
tree
2020-06-23
Pas
c
al Merz
R
e
f
a
c
to
r
simul
a
tor co
m
parison
tests
commit
|
commitdiff
|
tree
2020-06-18
Pascal
Merz
M
o
du
l
ar simulator: Separate
trajectory element
a
nd
.
.
.
commit
|
commitdiff
|
tree
2020-06-17
Pascal Merz
F
ix styl
e
e
rrors
i
n
modu
l
ar simulat
o
r propagator
commit
|
commitdiff
|
tree
2020-05-04
Pas
c
a
l Merz
Catch e
r
r
o
rs
i
n v-re
s
cale a
n
d Parrinello-Rahman checkpo
i
n
t
ing
commit
|
commitdiff
|
tree
2020-04-23
Pascal Merz
Make boxdeformati
o
n indep
e
ndent of t_commrec
commit
|
commitdiff
|
tree
2020-04-22
Pascal Merz
Ma
k
e
i
nit_dires
i
ndep
e
ndent of t_commr
e
c
commit
|
commitdiff
|
tree
2020-04-17
Pascal
Merz
Make gl
o
b
al topology c
o
nst in ISi
m
u
lato
r
commit
|
commitdiff
|
tree
2020-04-14
Pascal
M
e
r
z
Make bonded interaction che
c
king
more robust (modular
.
.
.
commit
|
commitdiff
|
tree
2020-04-14
Pascal
M
e
rz
R
e
int
r
o
d
uce LJ Ewald tabl
e
s
commit
|
commitdiff
|
tree
2020-04-07
P
a
scal Merz
M
e
rge for
c
e
a
nd shellFC elem
e
nts
commit
|
commitdiff
|
tree
2020-04-07
Pa
s
cal Merz
Require explicit M
P
I_CO
M
M f
o
r gmx
_
bcast and gm
x
_
b
ar
r
i
e
r
commit
|
commitdiff
|
tree
2020-04-07
Pasc
a
l
M
e
rz
M
ake
glob
a
l
topology c
o
nstant in
e
nerg
y
Output
.
pr
i
ntAn
n
ea
l
ing
.
.
.
commit
|
commitdiff
|
tree
2020-04-07
Pasca
l
M
e
rz
Make gl
o
bal topology const in minimization
commit
|
commitdiff
|
tree
2020-04-06
Pascal M
e
rz
M
ake global top
o
log
y
c
o
nsta
n
t
i
n
mdoutf
commit
|
commitdiff
|
tree
2020-04-06
Pascal M
e
rz
Make bonded interaction checking more robust (modular
.
.
.
commit
|
commitdiff
|
tree
2020-04-03
Pascal Merz
F
i
x expande
d
ensemble on chec
k
point rest
a
rts
commit
|
commitdiff
|
tree
2020-02-27
Pascal M
e
rz
L
oosen
gmx
a
pi stopsignaler test
commit
|
commitdiff
|
tree
2020-02-27
P
a
scal Merz
Use lega
c
y code path
for t_grap
h
(modul
a
r simulator)
commit
|
commitdiff
|
tree
2020-02-27
Pa
s
cal
M
erz
Extract and expose function to det
e
rmine whe
t
he
r
mo
l
ecules
.
.
.
commit
|
commitdiff
|
tree
2020-02-26
Pascal Merz
Fix co
n
straint contri
b
u
tion t
o
dhdl (modul
a
r simulator)
commit
|
commitdiff
|
tree
2020-02-26
Pasc
a
l Merz
Fix calcu
l
ation of r
e
c
i
procal terms in rerun
commit
|
commitdiff
|
tree
2020-02-24
Pasc
a
l Merz
Us
e
ArrayRe
f
in compute_globals
commit
|
commitdiff
|
tree
2020-02-21
Pascal
Merz
Use le
g
acy code path f
o
r NMR restraints (m
o
dular simulator)
commit
|
commitdiff
|
tree
2020-02-21
P
ascal
Merz
Correct for skewe
d
box in non-DD modular simulat
o
r
commit
|
commitdiff
|
tree
2020-02-14
Pascal Merz
Expand test co
v
erag
e
of exa
c
t
continuation te
s
t
s
commit
|
commitdiff
|
tree
2020-02-14
P
a
sc
a
l Merz
Fix reading of checkpoi
n
ts w
i
th
P
a
rrine
l
lo
-
R
ahman
.
.
.
commit
|
commitdiff
|
tree
2020-02-14
Pa
s
c
a
l
M
erz
Fix Parrine
l
l
o
-Rahman scaling on initia
l
s
t
ep (modular
.
.
.
commit
|
commitdiff
|
tree
2020-02-14
Pascal M
e
rz
Mo
v
e modu
l
a
r
s
i
mulator d
e
c
is
i
on b
e
fore checkpoint lo
a
ding
commit
|
commitdiff
|
tree
2020-02-13
Pascal Merz
Fix
c
hec
k
NumberOfBondedIn
t
eractions
bug
commit
|
commitdiff
|
tree
2020-02-13
Pa
s
cal
M
erz
Exp
o
se v
s
ite
c
o
unt
i
ng
commit
|
commitdiff
|
tree
2020-02-05
Pascal Merz
Test
PaddedVect
o
r
to
A
r
rayRe
f
conve
r
sion
commit
|
commitdiff
|
tree
2020-02-05
Pas
c
al
M
erz
Minor improvements
t
o vcm
.
cpp
commit
|
commitdiff
|
tree
2020-02-05
Pascal Merz
Merge V
V
im
p
lementations of
ComputeGlobalsE
l
ement
commit
|
commitdiff
|
tree
2020-01-31
Pascal Merz
Modular simul
a
to
r
: Allow for
n
ullpt
r
i
n element list
.
.
.
commit
|
commitdiff
|
tree
2020-01-31
Pascal
M
erz
StatePr
o
pagatorData: Make const
b
o
x
ge
t
ter
s
const
f
u
ncti
o
ns
commit
|
commitdiff
|
tree
2020-01-31
Pascal Mer
z
M
a
k
e
t_
i
np
u
tr
e
c const
in
C
omputeGl
o
b
al
s
Elemen
t
commit
|
commitdiff
|
tree
2019-12-17
Pasc
a
l Merz
Fix exact continuation modular
simulator
commit
|
commitdiff
|
tree
2019-12-12
P
a
scal Merz
Test for expected outp
u
t files
commit
|
commitdiff
|
tree
2019-12-12
Pascal Me
r
z
Fix final
c
o
nfiguration writing
for
mod
u
lar simul
a
tor
commit
|
commitdiff
|
tree
2019-10-31
P
a
scal Merz
C
he
c
k for contradicting environment var
i
a
b
le
s
(
m
o
d
u
l
ar
.
.
.
commit
|
commitdiff
|
tree
2019-10-30
Pascal Merz
F
ix dox
y
g
e
n
f
or modular simulator
commit
|
commitdiff
|
tree
2019-10-30
Pascal M
e
rz
Fix
modular simulator docu
m
entation
commit
|
commitdiff
|
tree
2019-10-29
P
a
sc
a
l Merz
Fix co
m
patibility check o
f
modul
a
r s
i
m
u
lator
commit
|
commitdiff
|
tree
2019-10-27
Pascal Mer
z
En
a
b
l
e fo
r
ced rotation for mod
u
lar simu
l
ator
commit
|
commitdiff
|
tree
2019-10-23
Pasca
l
Mer
z
Correct for skewe
d
box before domain dec
o
m
p
osition
.
.
.
commit
|
commitdiff
|
tree
2019-10-23
P
a
sc
a
l Merz
Fix l
o
g writi
n
g (m
o
d
ular simula
t
or)
commit
|
commitdiff
|
tree
2019-10-23
P
a
s
c
al
M
erz
Adapt
enum to s
t
yle convention (modular
simul
a
t
o
r)
commit
|
commitdiff
|
tree
2019-10-23
Pa
s
cal
Merz
Sma
l
l imp
r
oveme
n
t to
Energy
E
lement
(modul
a
r simulator)
commit
|
commitdiff
|
tree
2019-10-22
Pascal
M
e
rz
Fi
x
stop condi
t
i
o
n handling (m
o
dular simulator
)
commit
|
commitdiff
|
tree
2019-10-22
Pasc
a
l
Merz
F
i
x signal prop
a
gation (modula
r
simulator)
commit
|
commitdiff
|
tree
2019-10-22
Pascal Merz
Fix
D
omDec
step (
m
odula
r
simulator)
commit
|
commitdiff
|
tree
2019-10-22
Pascal Merz
Fix
P
meLoad
B
al
a
nceHelpe
r
i
n
itial
i
zation (modular si
m
ulator)
commit
|
commitdiff
|
tree
2019-10-01
Pascal Merz
Output correct kinetic at last step (modular simulato
r
)
commit
|
commitdiff
|
tree
2019-09-23
Pasca
l
Merz
Parrinello-R
a
hma
n
for md-v
v
commit
|
commitdiff
|
tree
2019-09-23
P
asca
l
Merz
Pa
r
r
ine
l
lo-Ra
h
man barost
a
t for
m
odular
s
imu
l
ator (leap
.
.
.
commit
|
commitdiff
|
tree
2019-09-23
P
a
scal Merz
Z
e
ro pressure and virial te
n
s
o
r
s
at beginning of step
commit
|
commitdiff
|
tree
2019-09-23
Pascal M
e
rz
Introd
u
ce
FEP into mo
d
ular simulator
commit
|
commitdiff
|
tree
2019-09-23
Pascal Merz
Make CheckpointHelper sa
f
er and easier to
use
commit
|
commitdiff
|
tree
2019-09-23
P
ascal
Me
r
z
Fix v
r
escale thermostat i
n
t
egral (modular simu
l
ato
r
)
commit
|
commitdiff
|
tree
2019-09-20
Pascal Merz
Fix
r
e
starts in
m
odular simulator
commit
|
commitdiff
|
tree
2019-09-20
Pascal M
e
rz
Fix
d
o
m
dec for m
d
-vv modula
r
simula
t
or
commit
|
commitdiff
|
tree
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