Skip to content

Commit 7d9e3a0

Browse files
mwest1066mwest1066
committed
Update info for 2.6.0 release
1 parent b9029e9 commit 7d9e3a0

13 files changed

+708
-368
lines changed

‎.dockerignore

+7
Original file line numberDiff line numberDiff line change
@@ -2,8 +2,11 @@
22
*
33

44
# whitelist things to copy
5+
!ChangeLog.md
56
!CMakeLists.txt
67
!netcdf.cmake
8+
!README.md
9+
!doc/
710
!docker/
811
!src/
912
!test/
@@ -18,3 +21,7 @@ scenarios/2_urban_plume2/out
1821
scenarios/3_condense/out
1922
!scenarios/4_chamber
2023
scenarios/4_chamber/out
24+
!scenarios/5_coag_brownian
25+
scenarios/5_coag_brownian/out
26+
!scenarios/6_camp
27+
scenarios/6_camp/out

‎.github/workflows/doc.yml

+13
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,13 @@
1+
name: CI
2+
3+
on: [push, pull_request]
4+
5+
jobs:
6+
build:
7+
8+
runs-on: ubuntu-latest
9+
10+
steps:
11+
- uses: actions/checkout@v1
12+
- name: Build the testing docker image
13+
run: docker build -t partmc-doc -f Dockerfile.doc .

‎CMakeLists.txt

+3-3
Original file line numberDiff line numberDiff line change
@@ -7,9 +7,9 @@ project(PARTMC Fortran C)
77

88
set(PACKAGE_BUGREPORT "[email protected]")
99
set(PACKAGE_NAME "PartMC")
10-
set(PACKAGE_STRING "PartMC 2.5.0")
10+
set(PACKAGE_STRING "PartMC 2.6.0")
1111
set(PACKAGE_TARNAME "partmc")
12-
set(PACKAGE_VERSION "2.5.0")
12+
set(PACKAGE_VERSION "2.6.0")
1313

1414
######################################################################
1515
# options
@@ -26,7 +26,7 @@ option(ENABLE_C_SORT "Enable C sorting routines" OFF)
2626

2727
set(CPACK_SOURCE_GENERATOR "TGZ")
2828
SET(CPACK_SOURCE_PACKAGE_FILE_NAME "${PACKAGE_TARNAME}-${PACKAGE_VERSION}")
29-
set(CPACK_SOURCE_IGNORE_FILES "${CPACK_SOURCE_IGNORE_FILES};/.*~$;/[.].*/;/build/;/figures/;/scenarios/[^1234].*/;/doc/condensation/;/doc/deposition/;/doc/ship_track/;/old/;/tool/;/TODO;/CMakeCache.txt")
29+
set(CPACK_SOURCE_IGNORE_FILES "${CPACK_SOURCE_IGNORE_FILES};/.*~$;/[.].*/;/build/;/figures/;/scenarios/[^123456].*/;/doc/condensation/;/doc/deposition/;/doc/ship_track/;/old/;/tool/;/TODO;/CMakeCache.txt")
3030

3131
include(CPack)
3232

‎ChangeLog.md

+7-1
Original file line numberDiff line numberDiff line change
@@ -1,5 +1,5 @@
11

2-
__next version__ - XXXX-XX-XX
2+
2.6.0 - 2021-11-03
33

44
* Clean up README formatting (Matt West).
55

@@ -12,6 +12,12 @@ __next version__ - XXXX-XX-XX
1212

1313
* Add multiple groups for mixing state index calculations (Matt West).
1414

15+
* Add interface to CAMP chemistry library (Matt Dawson and Jeff Curtis).
16+
17+
* Fix typo in `do_init_equilibrate` (Sylwester Arabas).
18+
19+
* Add `scenarios/5_coag_brownian` (Zhonghua Zheng and Jeff Curtis).
20+
1521
2.5.0 - 2018-11-17
1622

1723
* Shift NetCDF CMake rules to `netcdf.cmake` (Matt West).

‎Dockerfile

+2
Original file line numberDiff line numberDiff line change
@@ -2,6 +2,8 @@ FROM fedora:33
22

33
RUN dnf -y update \
44
&& dnf -y install \
5+
less \
6+
tmux \
57
gcc-gfortran \
68
make \
79
netcdf-fortran-devel \

‎Dockerfile.doc

+16
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,16 @@
1+
FROM fedora:33
2+
3+
RUN dnf -y update \
4+
&& dnf -y install \
5+
less \
6+
tmux \
7+
make \
8+
doxygen-latex \
9+
graphviz \
10+
&& dnf clean all
11+
12+
# NOTE: Modify .dockerignore to whitelist files/directories to copy.
13+
COPY . /partmc/
14+
15+
RUN cd /partmc/doc \
16+
&& make

‎README.md

+75-52
Original file line numberDiff line numberDiff line change
@@ -4,16 +4,16 @@ PartMC
44

55
PartMC: Particle-resolved Monte Carlo code for atmospheric aerosol simulation
66

7-
[![Latest version](https://img.shields.io/github/tag/compdyn/partmc.svg?label=version)](https://github.com/compdyn/partmc/blob/master/ChangeLog.md) [![Docker build status](https://img.shields.io/docker/automated/compdyn/partmc.svg)](https://hub.docker.com/r/compdyn/partmc/builds/) [![Build Status](https://img.shields.io/travis/compdyn/partmc/master.svg)](https://travis-ci.org/compdyn/partmc) [![License](https://img.shields.io/github/license/compdyn/partmc.svg)](https://github.com/compdyn/partmc/blob/master/COPYING) [![DOI](https://zenodo.org/badge/24058992.svg)](https://zenodo.org/badge/latestdoi/24058992)
7+
[![Latest version](https://img.shields.io/github/tag/compdyn/partmc.svg?label=version)](https://github.com/compdyn/partmc/blob/master/ChangeLog.md) [![GitHub build](https://img.shields.io/github/workflow/status/compdyn/partmc/CI.svg)](https://github.com/compdyn/partmc/actions) [![License](https://img.shields.io/github/license/compdyn/partmc.svg)](https://github.com/compdyn/partmc/blob/master/COPYING) [![DOI](https://zenodo.org/badge/24058992.svg)](https://zenodo.org/badge/latestdoi/24058992)
88

9-
Version 2.5.0
10-
Released 2018-11-17
9+
Version 2.6.0
10+
Released 2021-11-03
1111

1212
**Source:** <https://github.com/compdyn/partmc>
1313

1414
**Homepage:** <http://lagrange.mechse.illinois.edu/partmc/>
1515

16-
**Cite as:** M. West, N. Riemer, J. Curtis, M. Michelotti, and J. Tian (2018) PartMC, [![version](https://img.shields.io/github/release/compdyn/partmc.svg?label=version)](https://github.com/compdyn/partmc), [![DOI](https://zenodo.org/badge/24058992.svg)](https://zenodo.org/badge/latestdoi/24058992)
16+
**Cite as:** M. West, N. Riemer, J. Curtis, M. Michelotti, and J. Tian (2021) PartMC, [![version](https://img.shields.io/github/release/compdyn/partmc.svg?label=version)](https://github.com/compdyn/partmc), [![DOI](https://zenodo.org/badge/24058992.svg)](https://zenodo.org/badge/latestdoi/24058992)
1717

1818
Copyright (C) 2005-2021 Nicole Riemer and Matthew West
1919
Portions copyright (C) Andreas Bott, Richard Easter, Jeffrey Curtis,
@@ -25,75 +25,97 @@ For details see the file COPYING or
2525

2626
**References:**
2727

28-
* N. Riemer, M. West, R. A. Zaveri, and R. C. Easter (2009),
28+
* N. Riemer, M. West, R. A. Zaveri, and R. C. Easter (2009)
2929
Simulating the evolution of soot mixing state with a
3030
particle-resolved aerosol model, _J. Geophys. Res._ 114(D09202),
3131
<http://dx.doi.org/10.1029/2008JD011073>.
32-
* N. Riemer, M. West, R. A. Zaveri, and R. C. Easter (2010),
32+
* N. Riemer, M. West, R. A. Zaveri, and R. C. Easter (2010)
3333
Estimating black carbon aging time-scales with a
34-
particle-resolved aerosol model, _J. Aerosol Sci._ 41(1), 143-158,
35-
<http://dx.doi.org/10.1016/j.jaerosci.2009.08.009>.
34+
particle-resolved aerosol model, _J. Aerosol Sci._ 41(1),
35+
143-158, <http://dx.doi.org/10.1016/j.jaerosci.2009.08.009>.
3636
* R. A. Zaveri, J. C. Barnard, R. C. Easter, N. Riemer, and M. West
37-
(2010), Particle-resolved simulation of aerosol size,
38-
composition, mixing state, and the associated optical and cloud
39-
condensation nuclei activation properties in an evolving urban
40-
plume, _J. Geophys. Res._ 115(D17210),
37+
(2010) Particle-resolved simulation of aerosol size, composition,
38+
mixing state, and the associated optical and cloud condensation
39+
nuclei activation properties in an evolving urban plume,
40+
_J. Geophys. Res._ 115(D17210),
4141
<http://dx.doi.org/10.1029/2009JD013616>.
42-
* R. E. L. DeVille, N. Riemer, and M. West, Weighted Flow
42+
* R. E. L. DeVille, N. Riemer, and M. West (2011) Weighted Flow
4343
Algorithms (WFA) for stochastic particle coagulation,
44-
_J. Comp. Phys._ 230(23), 8427-8451, 2011,
44+
_J. Comp. Phys._ 230(23), 8427-8451,
4545
<http://dx.doi.org/10.1016/j.jcp.2011.07.027>
46-
* J. Ching, N. Riemer, and M. West, Impacts of black carbon mixing
47-
state on black carbon nucleation scavenging: Insights from a
48-
particle-resolved model, _J. Geophys. Res._ 117(D23209), 2012,
46+
* J. Ching, N. Riemer, and M. West (2012) Impacts of black carbon
47+
mixing state on black carbon nucleation scavenging: Insights from
48+
a particle-resolved model, _J. Geophys. Res._ 117(D23209),
4949
<http://dx.doi.org/10.1029/2012JD018269>
50-
* M. D. Michelotti, M. T. Heath, and M. West, Binning for efficient
51-
stochastic multiscale particle simulations, _Multiscale
52-
Model. Simul._ 11(4), 1071-1096, 2013,
50+
* M. D. Michelotti, M. T. Heath, and M. West (2013) Binning for
51+
efficient stochastic multiscale particle simulations, _Multiscale
52+
Model. Simul._ 11(4), 1071-1096,
5353
<http://dx.doi.org/10.1137/130908038>
54-
* N. Riemer and M. West, Quantifying aerosol mixing state with
55-
entropy and diversity measures, _Atmos. Chem. Phys._ 13,
56-
11423-11439, 2013, <http://dx.doi.org/10.5194/acp-13-11423-2013>
54+
* N. Riemer and M. West (2013) Quantifying aerosol mixing state
55+
with entropy and diversity measures, _Atmos. Chem. Phys._ 13,
56+
11423-11439, <http://dx.doi.org/10.5194/acp-13-11423-2013>
5757
* J. Tian, N. Riemer, M. West, L. Pfaffenberger, H. Schlager, and
58-
A. Petzold, Modeling the evolution of aerosol particles in a ship
59-
plume using PartMC-MOSAIC, _Atmos. Chem. Phys._ 14, 5327-5347,
60-
2014, <http://dx.doi.org/10.5194/acp-14-5327-2014>
58+
A. Petzold (2014) Modeling the evolution of aerosol particles in
59+
a ship plume using PartMC-MOSAIC, _Atmos. Chem. Phys._ 14,
60+
5327-5347, <http://dx.doi.org/10.5194/acp-14-5327-2014>
6161
* R. M. Healy, N. Riemer, J. C. Wenger, M. Murphy, M. West,
6262
L. Poulain, A. Wiedensohler, I. P. O'Connor, E. McGillicuddy,
63-
J. R. Sodeau, and G. J. Evans, Single
64-
particle diversity and mixing state measurements,
65-
_Atmos. Chem. and Phys._ 14, 6289-6299,
66-
2014, <http://dx.doi.org/10.5194/acp-14-6289-2014>
67-
* J. H. Curtis, M. D. Michelotti, N. Riemer, M. Heath, and M. West,
68-
Accelerated simulation of stochastic particle removal processes
69-
in particle-resolved aerosol models, _J. Comp. Phys._ 322, 21-32,
70-
2016, <http://dx.doi.org/10.1016/j.jcp.2016.06.029>
71-
* J. Ching, N. Riemer, and M. West, Black carbon mixing state
63+
J. R. Sodeau, and G. J. Evans (2014) Single particle diversity
64+
and mixing state measurements, _Atmos. Chem. and Phys._ 14,
65+
6289-6299, <http://dx.doi.org/10.5194/acp-14-6289-2014>
66+
* J. H. Curtis, M. D. Michelotti, N. Riemer, M. Heath, and M. West
67+
(2016) Accelerated simulation of stochastic particle removal
68+
processes in particle-resolved aerosol models, _J. Comp. Phys._
69+
322, 21-32, <http://dx.doi.org/10.1016/j.jcp.2016.06.029>
70+
* J. Ching, N. Riemer, and M. West (2016) Black carbon mixing state
7271
impacts on cloud microphysical properties: Effects of aerosol
7372
plume and environmental conditions, _J. Geophys. Res._ 121(10),
74-
5990-6013, 2016 <http://dx.doi.org/10.1002/2016JD024851>
75-
* J. Ching, J. Fast, M. West, and N. Riemer, Metrics to quantify
76-
the importance of mixing state for CCN activity, _Atmos.
77-
Chem. and Phys._ 17, 7445-7458, 2017
73+
5990-6013, <http://dx.doi.org/10.1002/2016JD024851>
74+
* J. Ching, J. Fast, M. West, and N. Riemer (2017) Metrics to
75+
quantify the importance of mixing state for CCN activity, _Atmos.
76+
Chem. and Phys._ 17, 7445-7458,
7877
<http://dx.doi.org/10.5194/acp-17-7445-2017>
7978
* J. Tian, B. T. Brem, M. West, T. C. Bond, M. J. Rood, and
80-
N. Riemer, Simulating aerosol chamber experiments with the
79+
N. Riemer (2017) Simulating aerosol chamber experiments with the
8180
particle-resolved aerosol model PartMC, _Aerosol Sci. Technol._
82-
51(7), 856-867, 2017
83-
<http://dx.doi.org/10.1080/02786826.2017.1311988>
84-
* J. H. Curtis, N. Riemer, and M. West, A single-column
81+
51(7), 856-867, <http://dx.doi.org/10.1080/02786826.2017.1311988>
82+
* J. H. Curtis, N. Riemer, and M. West (2017) A single-column
8583
particle-resolved model for simulating the vertical distribution
8684
of aerosol mixing state: WRF-PartMC-MOSAIC-SCM v1.0,
87-
_Geosci. Model Dev._ 10, 4057-4079, 2017
85+
_Geosci. Model Dev._ 10, 4057-4079,
8886
<http://dx.doi.org/10.5194/gmd-10-4057-2017>
89-
* J. Ching, M. West, and N. Riemer, Quantifying impacts of aerosol
90-
mixing state on nucleation-scavenging of black carbon aerosol
91-
particles, _Atmosphere_ 9(1), 17, 2018
87+
* J. Ching, M. West, and N. Riemer (2018) Quantifying impacts of
88+
aerosol mixing state on nucleation-scavenging of black carbon
89+
aerosol particles, _Atmosphere_ 9(1), 17,
9290
<http://dx.doi.org/10.3390/atmos9010017>
93-
* M. Hughes, J. K. Kodros, J. R. Pierce, M. West, and N. Riemer,
94-
Machine learning to predict the global distribution of aerosol
95-
mixing state metrics, _Atmosphere_ 9(1), 15, 2018
91+
* M. Hughes, J. K. Kodros, J. R. Pierce, M. West, and N. Riemer
92+
(2018) Machine learning to predict the global distribution of
93+
aerosol mixing state metrics, _Atmosphere_ 9(1), 15,
9694
<http://dx.doi.org/10.3390/atmos9010015>
95+
* R. E. L. DeVille, N. Riemer, and M. West (2019) Convergence of a
96+
generalized Weighted Flow Algorithm for stochastic particle
97+
coagulation, _Journal of Computational Dynamics_ 6(1), 69-94,
98+
<http://dx.doi.org/10.3934/jcd.2019003>
99+
* N. Riemer, A. P. Ault, M. West, R. L. Craig, and J. H. Curtis
100+
(2019) Aerosol mixing state: Measurements, modeling, and impacts,
101+
_Reviews of Geophysics_ 57(2), 187-249,
102+
<http://dx.doi.org/10.1029/2018RG000615>
103+
* C. Shou, N. Riemer, T. B. Onasch, A. J. Sedlacek, A. T. Lambe,
104+
E. R. Lewis, P. Davidovits, and M. West (2019) Mixing state
105+
evolution of agglomerating particles in an aerosol chamber:
106+
Comparison of measurements and particle-resolved simulations,
107+
_Aerosol Science and Technology_ 53(11), 1229-1243,
108+
<http://dx.doi.org/10.1080/02786826.2019.1661959>
109+
* J. T. Gasparik, Q. Ye, J. H. Curtis, A. A. Presto, N. M. Donahue,
110+
R. C. Sullivan, M. West, and N. Riemer (2020) Quantifying errors
111+
in the aerosol mixing-state index based on limited particle
112+
sample size, _Aerosol Science and Technology_ 54(12), 1527-1541,
113+
<http://dx.doi.org/10.1080/02786826.2020.1804523>
114+
* Z. Zheng, J. H. Curtis, Y. Yao, J. T. Gasparik, V. G. Anantharaj,
115+
L. Zhao, M. West, and N. Riemer (2021) Estimating submicron
116+
aerosol mixing state at the global scale with machine learning
117+
and earth system modeling, _Earth and Space Science_ 8(2),
118+
e2020EA001500, <http://dx.doi.org/10.1029/2020EA001500>
97119

98120

99121
Running PartMC with Docker
@@ -142,6 +164,7 @@ Required dependencies:
142164

143165
Optional dependencies:
144166

167+
* CAMP chemistry code - <https://github.com/open-atmos/camp>
145168
* MOSAIC chemistry code version 2012-01-25 - Available from Rahul
146169
Zaveri - <[email protected]>
147170
* MPI parallel support - <http://www.open-mpi.org/>
@@ -162,12 +185,12 @@ Installation
162185

163186
2. Unpack PartMC:
164187

165-
tar xzvf partmc-2.5.0.tar.gz
188+
tar xzvf partmc-2.6.0.tar.gz
166189

167190
3. Change into the main PartMC directory (where this README file is
168191
located):
169192

170-
cd partmc-2.5.0
193+
cd partmc-2.6.0
171194

172195
4. Make a directory called `build` and change into it:
173196

0 commit comments

Comments
 (0)