Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

Stokesian Dynamics #220

Merged
merged 65 commits into from Apr 17, 2015
Merged

Stokesian Dynamics #220

merged 65 commits into from Apr 17, 2015

Conversation

dschwoerer
Copy link
Contributor

With testcases and documentation
The SD implementation includes:

  • lubrication correction
  • Ewald summation for PBCs
  • thermalization

@dschwoerer
Does not run, but compiles. integrate_sd can be called. Has not imple…
a5c0555 
…mented Temp > 0.
@dschwoerer
should work, but is still slow
c03275e
@dschwoerer
optimized the kernel generating the matrizes
1918636
@dschwoerer
changed to new solver (using magma)
743c9ce
@dschwoerer
new: * iterative solver * avoids double counting of R_2B^inf * and more
be14030
@dschwoerer
works now without magma
0f75658
@dschwoerer
new:
9643091 
 * iterative solver
 * avoids double counting of R_2B^inf
 * and more
@dschwoerer
added nearfield force part for brownian motion
b9f2003
@dschwoerer
Merge commit 'b9f2003cb3c6ab56f68d52638ba458c951637478'
2567967 
Conflicts:
	src/integrate_sd.cpp
	src/integrate_sd_cuda.cu
	src/tcl/integrate_sd_tcl.cpp
@dschwoerer
Merge branch 'master' of git://github.com/espressomd/espresso
fe35c42 
Conflicts:
	src/Makefile.am
	src/global.cpp
	src/global.hpp
	src/tcl/initialize_interpreter.cpp
@dschwoerer
worked on brownian motion
48c90dd
@dschwoerer
added GMRes Iterative solver
b62c514 
additional BICGStab and GMRes have precondioner
@dschwoerer
Merge branch 'master' of git://github.com/espressomd/espresso
becb3b0 
Conflicts:
	src/Makefile.am
	src/core/global.cpp
	src/core/global.hpp
	src/tcl/initialize_interpreter.cpp
@dschwoerer
* preconditioner free matrix inversion is now done without matrix mat…
8b9f7b5 
…ix multiplication

* periodic boundary conditions are missing, rest should work
@dschwoerer
Merge branch 'master' of git://github.com/espressomd/espresso
0b1dfea
@dschwoerer
Merge branch 'master' of https://github.com/dschwoerer/espresso
01797a0
@dschwoerer
small changes
2b1af52
@dschwoerer
Merge branch 'master' of git://github.com/espressomd/espresso
7a07e49 
Conflicts:
	src/core/Makefile.am
@dschwoerer
Merge branch 'master' of git://github.com/espressomd/espresso
0f91251 
Conflicts:
	src/core/Makefile.am
@dschwoerer
seems to work
b3d0b94
@dschwoerer
Merge branch 'master' of /home/dschwoerer/soft/espresso/espresso-main
babf68d
@dschwoerer
Merge branch 'master' of git://github.com/espressomd/espresso
d3d03b9 
Conflicts:
	src/core/global.cpp
@dschwoerer
Merge branch 'master' of git://github.com/espressomd/espresso
35f4cfe
@dschwoerer
first try of an wavespace / realspace splitted aproach which should b…
0e364da 
…e O(N^3/2)
@dschwoerer
Merge branch 'master' of git://github.com/espressomd/espresso
0d030b9 
Conflicts:
	src/core/global.cpp
	src/core/global.hpp
@dschwoerer
* ewald summation is implemented
74384fe 
* speed of wavespace part is fine
* splitted code in several files
@dschwoerer
added documentation of Stokesian Dynamics
075aa92
@dschwoerer
fixed bugs in the ewald summation
7a65c19
@dschwoerer
Merge branch 'master' of git://github.com/espressomd/espresso
529e2bc
@dschwoerer
small changes
e7777d3
@dschwoerer
Merge branch 'master' of https://github.com/espressomd/espresso
e2123db
@dschwoerer
fixed warnings in correlator
2e8a09b
@dschwoerer
tiny fix in ug
4b8ec88
@dschwoerer
speedup of sd ewald sum
a26b86c
@dschwoerer
Merge branch 'master' of /home/dschwoerer/soft/espresso/espresso-main
5675a5d 
Conflicts:
	src/tcl/statistics_observable_tcl.cpp
@dschwoerer
Merge branch 'master' of https://github.com/espressomd/espresso
a9d07aa 
Conflicts:
	testsuite/correlation_checkpoint.tcl
@dschwoerer
added SD features to features.def
f97c3a4
@dschwoerer
added higher modes in structure facture fast
8423b4d
@dschwoerer
Fixes in SD and correlator checkpointing
2e70b2f
@dschwoerer
fix in brownian near field force
3e7016f
@dschwoerer
Merge branch 'master' of hs:repos/espresso
0300ca8
@dschwoerer
cleanup fixes
84fd2ff
@dschwoerer
Merge branch 'master' of https://github.com/espressomd/espresso
7728eae
@dschwoerer
tiny fix
7ec5e9e
@dschwoerer
compile fix
f5bf8f2
@dschwoerer
improved documentation
3e24215
@dschwoerer
Added testcases for Stokesian Dynamics
32c1b54
@dschwoerer
Fixed testcase: Added check that PBC are compiled in
af71437
@dschwoerer
Merge branch 'master' of https://github.com/espressomd/espresso
9ffd8e4
@dschwoerer
Merge branch 'master' of /home/dschwoerer/soft/espresso/espresso-main
a1ee606 
Conflicts:
	doc/ug/setup.tex
	src/core/thermostat.hpp
	src/tcl/Makefile.am
	src/tcl/thermostat_tcl.cpp
@dschwoerer
fix for GHMC
42e3b35
@dschwoerer
fixed particle counting if virtual sites are enabled
d8eaf92
@dschwoerer
fixed requirements for testcases
77b36ee
@dschwoerer
remove ADDITIONAL_CHECKS from integrate_sd.cpp
1c7495f
@dschwoerer
remove ADDITIONAL_CHECKS from integrate_sd.cpp
22eb46c
@dschwoerer
removed duplicate of sanity checks
cb7e37e
@dschwoerer
added documentation for arpack as requirement
e3db64b
fweik added a commit that referenced this pull request Apr 17, 2015
@fweik
Merge pull request #220 from dschwoerer/master
354b8e6 
Stokesian Dynamics
@fweik fweik merged commit 354b8e6 into espressomd:master Apr 17, 2015
jngrad pushed a commit to jngrad/espresso that referenced this pull request Jan 22, 2020
@bogdan-tanygin
Merge pull request espressomd#220 from psci2195/bd-merge-3
e4728c9 
Bd merge 3
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Reviewers
No reviews
Assignees
No one assigned
Labels
None yet
Projects
None yet
Milestone
No milestone
Development

Successfully merging this pull request may close these issues.

None yet
2 participants
@dschwoerer @fweik