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CMake 0.34% Batchfile 0.70% Smarty 0.99% TeX 0.19% Shell 0.68% HTML 50.62% CSS 0.72% Scheme 0.19% Makefile 0.74% C 1.90% C++ 41.67% Python 0.10% Max 0.30% M4 0.31% PowerShell 0.08% AMPL 0.04% Scilab 0.12% BASIC 0.25% Euphoria 0.05% Assembly 0.02%

phreeqc

phreeqc3's Introduction

PHREEQC

Description

PHREEQC Version 3 is a computer program written in the C++ programming language that is designed to perform a wide variety of aqueous geochemical calculations. PHREEQC implements several types of aqueous models including two ion-association aqueous models.

Disclaimer

This software is preliminary or provisional and is subject to revision. It is being provided to meet the need for timely best science. The software has not received final approval by the U.S. Geological Survey (USGS). No warranty, expressed or implied, is made by the USGS or the U.S. Government as to the functionality of the software and related material nor shall the fact of release constitute any such warranty. The software is provided on the condition that neither the USGS nor the U.S. Government shall be held liable for any damages resulting from the authorized or unauthorized use of the software.

phreeqc3's People

Contributors

Stargazers

Watchers

Forkers

liuhai84 scharlton2 dlparkhurst bentontripp alanliska nattia-chen ondrejhasnik chemsoftware

phreeqc3's Issues

tests 258 and 338 fail on macOS

$ ctest -C Release -I 1,1,1,258,338
Test project /Users/charlton/source/repos/coupled/phreeqc3/_build
    Start   1: ex1
1/3 Test   #1: ex1 ..............................   Passed    0.04 sec
    Start 258: mytest.P_Vm
2/3 Test #258: mytest.P_Vm ......................***Failed    0.23 sec
    Start 338: mytest.rho_H3PO4
3/3 Test #338: mytest.rho_H3PO4 .................***Failed    0.04 sec

33% tests passed, 2 tests failed out of 3

Total Test time (real) =   0.34 sec

The following tests FAILED:
	258 - mytest.P_Vm (Failed)
	338 - mytest.rho_H3PO4 (Failed)
Errors while running CTest
Output from these tests are in: /Users/charlton/source/repos/coupled/phreeqc3/_build/Testing/Temporary/LastTest.log
Use "--rerun-failed --output-on-failure" to re-run the failed cases verbosely.

Files

P_Vm.zip

rho_H3PO4.zip

Update subtree splitting and merging for main/develop branches

Test on coupled-test (set ${GROUP} to coupled-test)???

Convert to github actions ???

on code.chs.usgs.gov (Gitlab)
rename master to main for all pipeline repos
copy main to develop for all pipeline repos

update all .gitlab-ci.yml to work on the develop branch only

Add database/PHREEQC_ThermoddemV1.10_15Dec2020.dat to dist

check ThermoChimie7d_sit_JUNE_2011.dat encoding

see usgs-coupled/iphreeqc#13

Consider using cmake-format cmake-lint for pre-commits

Move phreeqc-chm-windows-git to github-actions

This issue was moved from usgs-coupled-subtrees/phreeqc3-HTMLversion#1

Merge conflicts #2408420

Running with gitlab-runner 15.10.1 (dcfb4b66)
  on chs-shared-runners-i-046ce0ed6313[2](https://code.chs.usgs.gov/coupled/phreeqc3/-/jobs/2408420#L2)6747 [3](https://code.chs.usgs.gov/coupled/phreeqc3/-/jobs/2408420#L3)dxCawZT, system ID: s_2635aaf9f0a1
Preparing the "docker+machine" executor
00:07
Using Docker executor with image code.chs.usgs.gov:5001/coupled/containers/buildpack-deps:bionic-scm ...
Authenticating with credentials from job payload (GitLab Registry)
Pulling docker image code.chs.usgs.gov:5001/coupled/containers/buildpack-deps:bionic-scm ...
Using docker image sha256:cbed96d2ebf25728c8b52b136ad931[4](https://code.chs.usgs.gov/coupled/phreeqc3/-/jobs/2408420#L4)cc1dabb3b82f97c633beb27d7b3786b80 for code.chs.usgs.gov:[5](https://code.chs.usgs.gov/coupled/phreeqc3/-/jobs/2408420#L5)001/coupled/containers/buildpack-deps:bionic-scm with digest code.chs.usgs.gov:5001/coupled/containers/buildpack-deps@sha25[6](https://code.chs.usgs.gov/coupled/phreeqc3/-/jobs/2408420#L6):4b53[7](https://code.chs.usgs.gov/coupled/phreeqc3/-/jobs/2408420#L7)16f1b6f2bd3039707fa25a200b793825825f4f7d1adb4e3d534ac0d9d0d ...
Preparing environment
00:01
Running on runner-3dxcawzt-project-4256-concurrent-0 via runner-3dxcawzt-gitlab-runner-1681144741-cbf8231d...
Getting source from Git repository
00:24
Fetching changes with git depth set to 50...
Initialized empty Git repository in /builds/coupled/phreeqc3/.git/
Created fresh repository.
Checking out 60c6d5d0 as detached HEAD (ref is master)...
Skipping Git submodules setup
Executing "step_script" stage of the job script
01:14
Using docker image sha256:cbed96d2ebf25728c8b52b136ad9314cc1dabb3b82f97c633beb27d7b3786b80 for code.chs.usgs.gov:5001/coupled/containers/buildpack-deps:bionic-scm with digest code.chs.usgs.gov:5001/coupled/containers/buildpack-deps@sha256:4b53716f1b6f2bd3039707fa25a200b793825825f4f7d1adb4e3d534ac0d9d0d ...
$ eval $(ssh-agent -s)
Agent pid 14
$ echo "${SSH_PRIVATE_KEY_ENC}" | base64 --decode | tr -d '\r' | ssh-add -
Identity added: (stdin) ([email protected])
$ mkdir -p ~/.ssh
$ chmod 700 ~/.ssh
$ ssh-keyscan ${CI_SERVER_HOST} >> ~/.ssh/known_hosts
# code.chs.usgs.gov:22 SSH-2.0-OpenSSH_7.4
# code.chs.usgs.gov:22 SSH-2.0-OpenSSH_7.4
# code.chs.usgs.gov:22 SSH-2.0-OpenSSH_7.4
$ chmod 644 ~/.ssh/known_hosts
$ git config --global user.email "[email protected]"
$ git config --global user.name "Darth Vader"
$ cd ..
$ rm -rf ${CI_PROJECT_NAME}
$ git clone git@${CI_SERVER_HOST}:${CI_PROJECT_PATH}.git
Cloning into 'phreeqc3'...
Warning: Permanently added the ECDSA host key for IP address '10.12.1.165' to the list of known hosts.
remote: warning: ignoring extra bitmap file: '/var/opt/gitlab/git-data/repositories/@pools/[9](https://code.chs.usgs.gov/coupled/phreeqc3/-/jobs/2408420#L9)c/fd/9cfd3c755be26b4e1645918e2a64a26e3d851ede421e0b257f783b443bc443d1.git/objects/pack/multi-pack-index'        
Checking out files: 100% (3494/3494), done.
$ cd ${CI_PROJECT_NAME}
$ #!/bin/bash -ex # collapsed multi-line command
remote: warning: ignoring extra bitmap file: '/var/opt/gitlab/git-data/repositories/@pools/aa/e0/aae02129362d611717b6c00ad8d73bf820a0f6d88fca8e515cafe78d3a335965.git/objects/pack/multi-pack-index'        
From code.chs.usgs.gov:coupled/subtrees/phreeqc3-doc
 * branch              master     -> FETCH_HEAD
Subtree is already at commit c3ed55b0e443c4ea3b85ecfc4fd8c78416a53321.
From code.chs.usgs.gov:coupled/subtrees/phreeqc3-HTMLversion
 * branch              master     -> FETCH_HEAD
Subtree is already at commit ca6d59b0762e50d66ffbea82f9a63666bf573312.
From code.chs.usgs.gov:coupled/subtrees/phreeqc3-database
 * branch              master     -> FETCH_HEAD
Subtree is already at commit 91aa5fd89b2f211b1dc85020c227df1a35676318.
remote: warning: ignoring extra bitmap file: '/var/opt/gitlab/git-data/repositories/@pools/43/c7/43c727ee4fc7250574d2ef90cfa16626388a10e1b30d36ece1c272953ad2ed9e.git/objects/pack/multi-pack-index'        
From code.chs.usgs.gov:coupled/subtrees/phreeqc3-src
 * branch              master     -> FETCH_HEAD
Auto-merging src/tally.cpp
CONFLICT (content): Merge conflict in src/tally.cpp
Auto-merging src/spread.cpp
CONFLICT (content): Merge conflict in src/spread.cpp
Auto-merging src/prep.cpp
CONFLICT (content): Merge conflict in src/prep.cpp
Auto-merging src/pitzer.cpp
CONFLICT (content): Merge conflict in src/pitzer.cpp
Auto-merging src/model.cpp
CONFLICT (content): Merge conflict in src/model.cpp
Auto-merging src/gases.cpp
CONFLICT (content): Merge conflict in src/gases.cpp
Auto-merging src/cl1.cpp
Automatic merge failed; fix conflicts and then commit the result.
Cleaning up project directory and file based variables
00:01
ERROR: Job failed: exit code 1

Missing database file causes infinite loop in ctest

see https://github.com/usgs-coupled/phreeqc3/actions/runs/3860140795

test (macos-latest):
https://github.com/usgs-coupled/phreeqc3/actions/runs/3860140795/jobs/6580305486#step:6:924

macos-latest was the only job to finish but also created a 3.75 GB artifact. The results weren't posted to
https://my.cdash.org/index.php?project=phreeqc3.
probably rejected due to size.

numdiff: PR_error_incremental_101.sel: No such file or directory

CMakeLists.txt is missing PR_error_incremental

Visual Studio before 2015 doesn't implement snprintf

for possible fix see:
https://stackoverflow.com/questions/2915672/snprintf-and-visual-studio-2010

mytest/current_analytical_101.sel isn't checked in

mytest/current_analytical_101.sel hasn't been checked in although
current_analytical creates it

Strange results for mytest/P_Vm

Results of running tag v3.7.3 version of mytest/P_Vm:
old.zip

Results of running 421faf6 version of mytest/P_Vm:
new.zip

each folder contains the output of each of the following:

phreeqc-3.7.3-15968-x64/    original windows distribution
421faf60/                   compiled from 421faf60 commit (latest version)
v3.7.3/                     compiled using the same source as the distribution (using 421faf60 cmake files)

phreeqc-3.7.3-15968-x64 fails to run newer version of P_Vm
except for timing, both of the cmake builds yield the same results for each input file on Windows (vs2019)

https://github.com/usgs-coupled/phreeqc3/blob/master/print.cpp#L1461

but it should be:

https://github.com/usgs-coupled/phreeqc3/blob/master/src/print.cpp#L1461

might be able to fix by modifying the way source files are included in the
CMakeLists.txt files

Some tests are failing due to time limits

Timed out @ 15 minutes on Darwin
mytest.current_analytical 484086c

Timed out @ 10 minutes on Linux
examples.ex15
examples.ex15a
examples.ex15b
mytest.colloid_U
mytest.ex15.cvode