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Author SHA1 Message Date
iafoss bdbbe00ec7 Merge branch 'master' into feature-cnt 2020-03-06 18:41:38 -05:00
Axel Kohlmeyer 1fb54c307c
Merge pull request #1918 from akohlmey/collected-small-fixes 
Collected small fixes for the next patch
 2020-03-05 15:16:50 -05:00
Axel Kohlmeyer 5a3a5d86d4
reduce compiler warnings and avoid clash with KOKKOS 2020-03-05 14:27:33 -05:00
Axel Kohlmeyer fb3a8f5bb1
Merge pull request #1909 from giacomofiorin/colvars-update 
Update Colvars to version 2020-02-27
 2020-03-05 10:18:01 -05:00
Miguel Dias Costa 8765b14377 add EPYC to KOKKOS_ARCH_LIST 2020-03-01 13:45:06 +08:00
Giacomo Fiorin 7be004512f Update Colvars to version 2020-02-27 
This update contains several small new features or usability improvements.
    Descriptions and authorship information can be accessed from the pull
    requests listed below.

    Allow setting sigma parameter directly for metadynamics
    https://github.com/Colvars/colvars/pull/325

    Remove default values for lowerWall and upperWall legacy keywords
    https://github.com/Colvars/colvars/pull/324

    biasActualColvar option to bypass extended-Lagragian for a bias
    https://github.com/Colvars/colvars/pull/321

    Flexible restart-reading
    https://github.com/Colvars/colvars/pull/320
 2020-02-27 19:55:31 -05:00
Axel Kohlmeyer 0db0d5408a
update instructions for in qmmm README to cover both build systems and include more details 2020-02-20 16:59:06 +01:00
Vsevak 3298a86bd9 Reduce redundant copying using UCL_H_Vec::view 2020-02-20 18:32:52 +03:00
Axel Kohlmeyer 8a52e5dbe7
fix logic error in generic Install.py script when a Makefile.lammps is missing 2020-02-19 18:10:32 +01:00
mariella ippolito cc3a7c37cb more lib compilation updates 2020-02-18 11:16:08 +01:00
mariella ippolito 36458a95b7 Updated 2020-02-18 10:59:51 +01:00
mariella ippolito 387a283157 more lib compilation updates 2020-02-18 10:55:13 +01:00
mariella ippolito 82b57bd3b8 Upfated Makefile.foo inside lib/qmmm 2020-02-18 10:47:04 +01:00
Axel Kohlmeyer 4cacc4701d
update plumed support to include version 2.6.0. Fix bug in API check 2020-02-13 16:03:58 +01:00
Vsevak d024b3d340 Add shared memory optimization 2020-02-12 01:35:44 +03:00
iafoss 0204bf286b CNT package 
The tubular potential model (TPM) force field for Carbon Nanotubes (CNTs) package.
 2020-02-06 16:50:38 -05:00
Vsevak 33fc22b752 Fix echo in Makefile 2020-02-03 01:55:20 +03:00
Vsevak 9e8806bd22 Addition to lib/gpu/README for HIP 2020-01-31 21:26:52 +03:00
Giacomo Fiorin 9427fc50a5 Update Colvars library to version 2020-01-27 
One new feature (arithmetic path variables) and several smaller enhancements
or bugfixes.

    Fix error check when loading an old state file
    https://github.com/Colvars/colvars/pull/317

    Get default values for grid boundaries when available
    https://github.com/Colvars/colvars/pull/310

    Allow redefining existing index groups (warn when this happens)
    https://github.com/Colvars/colvars/pull/302

    Simplified replica communication syntax in metadynamics
    https://github.com/Colvars/colvars/pull/301

    Obtain the bias_energy for ABF biases
    https://github.com/Colvars/colvars/pull/294

    Fix reading path file with vector CVCs
    https://github.com/Colvars/colvars/pull/288

    Fix segfault at deleting CVBasedPath
    https://github.com/Colvars/colvars/pull/286

    Parrinello's (arithmetic) pathCV in CV space
    https://github.com/Colvars/colvars/pull/274

    Fix race condition when starting a bundle of walkers
    https://github.com/Colvars/colvars/pull/279
 2020-01-28 14:15:05 -05:00
Vsevak 66c5fa2abd Merge 'gpu_hip_port' into master 2020-01-28 20:35:08 +03:00
Vsevak 43a9936241 Fix tagint usage 2020-01-20 03:38:58 +03:00
Vsevak f69a17dd3a Reduce unnecessary data exchanges 2020-01-19 02:05:16 +03:00
Axel Kohlmeyer 514271c984
recover compilation with -DLAMMPS_BIGBIG and fix whitespace and formatting issues 2020-01-08 17:57:54 -05:00
Axel Kohlmeyer 18a0cd3ead
Merge pull request #1817 from akohlmey/collected-small-fixes 
Collected small bugfixes and updates
 2020-01-08 17:16:34 -05:00
Axel Kohlmeyer d3eed9dba4
Merge pull request #1752 from ndtrung81/gpu-mem-leak-init 
Fixed bugs with kernel (re)compiling when the global device got clear and reinitialized
 2020-01-08 16:17:13 -05:00
Axel Kohlmeyer 6e2c3b7ce9
Merge branch 'master' into collected-small-fixes 2020-01-08 16:14:19 -05:00
Axel Kohlmeyer 481c647889
Merge pull request #1776 from Vsevak/tip4p_gpu 
GPU support for lj/cut/tip4p/long pair style
 2020-01-08 15:35:39 -05:00
Axel Kohlmeyer 00dce6b198
Merge branch 'master' into gpu-mem-leak-init 2020-01-08 14:26:03 -05:00
Vsevak e8a941a0b9 Remove unnecessary data transfer from tip4p/gpu pairstyle init 
Such data transfer is performed at each timestep, so it does not belong to the initialization
 2020-01-08 01:48:47 +03:00
Axel Kohlmeyer 66a473455e
silence warnings from generic OpenCL header files (as seen on Fedora 31) 2020-01-06 17:34:26 -05:00
Vsevak 337b0fd649 Fix 'sametag' transfer 2019-12-22 20:20:12 +03:00
Trung Nguyen 4c3ec145f3 Corrected the wrong use of the stubs path in -rpath 2019-12-17 14:05:39 -06:00
Trung Nguyen 7e8a04d985 More minor update to README 2019-12-12 09:57:49 -06:00
Trung Nguyen 99ba15bf6a Updated README and added -L$(CUDA_HOME)/lib64/stubs to the Makefile's 2019-12-11 16:29:42 -06:00
Vsevak a3fca53e97 Separate the computation of newsite into another kernel 
This eliminates the need for thread fence and makes the calculation stable on GTX1070 (CUDA and OpenCL) and TitanV
 2019-12-07 15:54:20 +03:00
Vsevak 4a51e1660f Add thread fence in kernel to fix Volta indeterminacy 2019-12-07 01:16:39 +03:00
Vsevak a2f9fa8e78 Separate the computation of hneigh into another kernel 
Simplify the main GPU kernel and add another kernel 'k_pair_reneigh'. It works good on GTX1070 (Pascal), but still there is a problem with non-deterministic results on Volta.

I reimplement BaseCharge::compute methods in the child class LJ_TIP4PLong to correctly embed a new kernel in the code.

Also commit includes some codestyle fixes.
 2019-12-06 21:41:02 +03:00
Vsevak 66a076b819 Delete "float.h" from TIP4P GPU kernel for better OpenCL compatibility 
According to Khronos OpenCL docs, "The C99 standard headers <...>, float.h, <...> are not available and cannot be included by a program"
 2019-11-27 19:49:12 +03:00
Vsevak 4febc7f794 Add copyright and fix style 2019-11-18 02:01:32 +03:00
Vsevak ca8d1ac2ff Simplify tip4p GPU memory resize using 'resize_ib' 2019-11-18 02:01:32 +03:00
Vsevak f803ba5655 Add shfl_xor sum to kernel for ARCH>=300 2019-11-12 21:35:36 +03:00
Vsevak 64bdc59623 Implement GPU pair style lj/cut/tip4p/long/gpu 
Source code, Makefiles and Install for GPU-accelerated TIP4P pair style.
It is implemented as a part of the standard GPU package.
The style is compatible with the standard  lj/cut/tip4p/long.
Also, this commit modifies "atom.h" just to
add a getter for variable 'max_same'.
 2019-11-10 02:38:58 +03:00
Trung Nguyen e119bffcca Fixed bugs with kernel (re)compiling when the global device got cleared and then reinitialized 2019-10-31 01:15:53 -05:00
Michael Brown a0d74ca2ae Bug fix for gay-berne potential when mu != 1.0. 2019-10-27 22:31:00 -07:00
Axel Kohlmeyer b631362137
Merge pull request #1735 from ndtrung81/gpu-mem-leak-init 
Gpu mem leak with init invoked multiple times
 2019-10-25 17:08:21 -04:00
Axel Kohlmeyer e7cb2f4cac
put back overly eager deleted code that is used without -DNDEBUG 2019-10-21 03:25:21 -04:00
Axel Kohlmeyer 08b55c4ca5
silence compiler warning 2019-10-20 19:00:54 -04:00
Axel Kohlmeyer c144b1af71
fix typos 2019-10-20 18:42:22 -04:00
Axel Kohlmeyer 6767fa5604
update supported plumed library to version 2.5.3 2019-10-20 16:27:32 -04:00
Axel Kohlmeyer 67512f8afc
remove bogus POEMS header files from AtC lib folder 2019-10-20 16:13:03 -04:00
Axel Kohlmeyer b705525734
resolve unused parameter warnings in USER-ATC package 2019-10-20 13:36:06 -04:00
Trung Nguyen 86f644979c Updated pppm 2019-10-20 00:18:28 -05:00
Trung Nguyen dfbee32575 Fixing issues with growing memory allocation with multiple init calls 2019-10-19 23:35:52 -05:00
Axel Kohlmeyer f4fcd2a911
flag that MESSAGE package is not compatible with -DLAMMPS_BIGBIG 2019-10-19 09:50:07 -04:00
Axel Kohlmeyer d684b70555
reduce compiler warnings in USER-AWPMD 2019-10-18 15:57:07 +02:00
Giacomo Fiorin 693e34b587 Print parsed compiler flags, some cosmetic changes for added consistency 2019-10-17 22:53:13 -04:00
Giacomo Fiorin c578e4e7fc Enable COLVARS_LEPTON for make, update build doc for USER-COLVARS 2019-10-17 22:48:57 -04:00
Giacomo Fiorin b6af3c7ad0 Conventional make tweaks to handle Lepton C++11 requirement 2019-10-14 16:05:45 -04:00
Giacomo Fiorin e04a18fc4f Upgrade Lepton library to version 2019-06-02 2019-10-14 16:05:45 -04:00
Axel Kohlmeyer b72215fe02
add support for automated checksumming of downloaded sources to kim api conventional build 2019-08-16 12:43:37 -04:00
Ryan S. Elliott 42711245a2 bump kim-api to 2.1.3 2019-08-16 10:08:23 -06:00
Axel Kohlmeyer 16bf916dd0
Merge pull request #1616 from akohlmey/fixes-for-stable 
Collected small fixes for stable release
 2019-08-05 16:48:50 -04:00
Giacomo Fiorin 97501f0946 Fix typo 2019-08-05 14:59:40 -04:00
Giacomo Fiorin 51ba9bd520 Bugfix for Colvars library (update to version 2019-08-05) 
Bugfix for group2CenterOnly (coordNum option):
https://github.com/Colvars/colvars/pull/278
 2019-08-05 14:14:33 -04:00
Axel Kohlmeyer 0774e92ece
use KIM-API 2.1.2 consistently with CMake and conventional build system 2019-08-03 06:40:31 -04:00
Axel Kohlmeyer 11198e9d29
Merge pull request #1607 from giacomofiorin/colvars-update 
Update Colvars to version 2019-08-01
 2019-08-02 10:43:13 -04:00
Giacomo Fiorin 52e2db44a1 Update Colvars to version 2019-08-01 
One new feature (geometric path variables) and bugfixes.

Minimize occurrence of file-read errors in multiple-walker metadynamics
https://github.com/Colvars/colvars/pull/276

Better error messages for RMSD
https://github.com/Colvars/colvars/pull/272

Ensemble-biased metadynamics documentation
https://github.com/Colvars/colvars/pull/261

Fix bug on multiple walkers metadynamics, pmf included twice
https://github.com/Colvars/colvars/pull/259

Implementation of the geometric path collective variables (C++11-only feature)
https://github.com/Colvars/colvars/pull/249
 2019-08-01 15:15:58 -04:00
Axel Kohlmeyer 2b288bc9e0
add missing mode keyword for substitution 2019-07-30 16:53:27 -04:00
Axel Kohlmeyer 882b2301bb
handle shared library extension on macosx for plumed runtime build 2019-07-30 16:48:50 -04:00
Axel Kohlmeyer 2d93a713e2
Merge branch 'master' into collected-small-changes 2019-07-30 14:14:11 -04:00
Axel Kohlmeyer 3fdadb5875
add configuration for linking VTK 7.1 on Ubuntu 18.04 2019-07-30 06:02:47 -04:00
Axel Kohlmeyer 7ab7691c51
update PLUMED support to version 2.5.2 2019-07-30 05:57:57 -04:00
Axel Kohlmeyer 6833d6def6
Merge branch 'master' into kim-simulator-models 
# Resolved Conflicts:
#	src/KIM/kim_query.cpp
#	src/KIM/pair_kim.cpp
 2019-07-29 20:43:10 -04:00
Axel Kohlmeyer 0f10c55c1c
avoid recursive header inclusion 2019-07-26 17:26:59 -04:00
Axel Kohlmeyer d59737299c
whitespace cleanup 2019-07-24 16:02:49 -04:00
Ryan S. Elliott be86db9dd9 Update /lib/kim stuff 2019-07-23 21:06:02 -05:00
Axel Kohlmeyer 320be3bcef
undo changes to poems library and package as they fail regression testing 2019-07-22 14:22:36 -04:00
Axel Kohlmeyer 68626f577b
Merge branch 'master' into improve-include-consistency 2019-07-12 19:59:56 -04:00
Axel Kohlmeyer e832b5d50b
make clang++ happy when trying to compile the GPU library 2019-07-12 15:42:16 -04:00
Axel Kohlmeyer 06dcc9e283
Merge branch 'master' into improve-include-consistency 
# Conflicts:
#	src/USER-MESO/atom_vec_tdpd.cpp
 2019-07-09 14:50:00 -04:00
Trung Nguyen 46a9772a6d Minor clean-up 2019-07-05 12:12:29 -05:00
Axel Kohlmeyer d07a49aeea
add missing prototypes 2019-07-05 11:37:21 -04:00
Trung Nguyen 49f27573a7 Fixed a bug in lj96 involving missing the special_lj factor 2019-07-03 23:44:33 -05:00
Axel Kohlmeyer e63fe1fe84
please POEMS library in namespace POEMS and remove "using namespace" from headers 2019-07-04 00:09:01 -04:00
Axel Kohlmeyer 42c31227d9
continuing to clean up include file lists 2019-07-01 15:59:16 -04:00
Axel Kohlmeyer 39f5b8c734
transform POEMS library to conform to IWYU conventions 2019-07-01 04:16:00 -04:00
Stan Moore ea2e73119d Update Kokkos library in LAMMPS to v2.9.00 2019-06-28 11:23:24 -06:00
Christoph Junghans 8c3d18520d add missing include needed on ppc64le 2019-06-26 10:45:31 -06:00
Axel Kohlmeyer 2f29bd29f4
Merge pull request #1430 from ndtrung81/gpu-neigh-hybrid 
Enable neighbor build on the device for pair hybrid substyles
 2019-06-17 14:12:40 -04:00
Axel Kohlmeyer b3f4e2055e
Merge pull request #1438 from giacomofiorin/colvars-update 
Update Colvars library to version 2019-04-26
 2019-05-06 12:08:50 -04:00
Giacomo Fiorin 7e00acce53 Update Colvars library to version 2019-04-26 
The following is list of relevant issues fixed and improvements:

Fix forces and missing output of runtime histogram for histogramRestraint
https://github.com/Colvars/colvars/pull/246

Use fix_modify to add configuration to Colvars:
https://github.com/Colvars/colvars/pull/216

Fix componentCoeff and name not working with orientationAngle components:
https://github.com/Colvars/colvars/issues/213

Fix 1-timestep offset with extendedLagrangian:
https://github.com/Colvars/colvars/pull/210

Changes to improve compiler support:
https://github.com/Colvars/colvars/pull/203

Fix ignored anisotropic cutoff3 for groupCoordNum:
https://github.com/Colvars/colvars/pull/202

New dipoleMagnitude variable:
https://github.com/Colvars/colvars/pull/198

Parser improvements:
https://github.com/Colvars/colvars/pull/196
 2019-04-30 13:46:37 -04:00
Richard Berger 8145c5028d Fix OpenCL compilation errors due to bad comments in macros 2019-04-30 00:44:12 -04:00
Trung Nguyen 4a4297591e Did some more cleanups 2019-04-17 12:04:31 -05:00
Trung Nguyen 1f43efc111 Cleaned up the changes in Device and the base class of the pair styles 2019-04-17 00:09:49 -05:00
Trung Nguyen c55009a0ac Enabled neighbor list build on the device with pair_style hybrid and hybrid/overlay 2019-04-16 23:30:25 -05:00
Axel Kohlmeyer c52a330a79
update USER-PLUMED support for version 2.5.1 and fix bug in Install.py script 2019-04-04 14:19:53 -04:00
Axel Kohlmeyer 265ad4512d
add sanity check on plumed pre-installed path location 2019-04-04 13:18:27 -04:00
Axel Kohlmeyer 1696432e82
resolve conflict between src/STUBS/mpi.h and lib/message/cslib/src/STUBS_MPI/mpi.h 2019-04-03 01:00:53 -04:00
Ryan S. Elliott 9d0e518cc5 Updates for kim-api-2.0.2 release 2019-03-28 15:35:22 -05:00
Axel Kohlmeyer 2f20581b29
Merge pull request #1374 from akohlmey/collected-small-fixes 
Collected small changes for the next patch release
 2019-03-25 13:15:45 -04:00
Axel Kohlmeyer cd6b23d104
explicitly request OpenCL version 1.2 compatibility when compiling GPU package kernels for OpenCL 2019-03-22 09:50:31 -04:00
Axel Kohlmeyer 741a7fe630
final touches to support compiling with libcurl transparently 2019-03-19 15:40:49 -04:00
Ryan S. Elliott b628e3b1b6 Update openkim.org urls in various places 2019-03-06 10:26:03 -06:00
Ryan S. Elliott 54e5c76333 Bump KIM API version to 2.0.1 2019-02-27 15:50:08 -06:00
Ryan S. Elliott e95cf4e917 Some various doc updates for kim-api support 2019-02-14 13:38:28 -06:00
Ryan S. Elliott 333154633b Merge branch 'master' into kim-v2-update 2019-02-14 13:29:50 -06:00
Axel Kohlmeyer 9ac908f05f
switch download server for voro++ from LBL to download.lammps.org, which seems much more reliable 2019-02-13 09:53:20 -05:00
Stan Moore 773476634b Update Kokkos library in LAMMPS to v2.8.00 2019-02-08 08:50:26 -07:00
Ryan S. Elliott 927dc262b2 Update CMake & Install.py for KIM API v2 2019-02-06 23:41:45 -06:00
Ryan S. Elliott d677335b23 Merge remote-tracking branch 'lammps/master' into kim-v2-update 2019-02-03 12:45:44 -06:00
Ryan S. Elliott a9b0fb9e9d Some adjustments to kim Install.py 2019-02-03 12:43:48 -06:00
Stan Moore 64834e4a3d Update Kokkos library 2019-02-01 12:45:54 -07:00
Axel Kohlmeyer 8ee1fefe19 add pointer to README and Manual to help. 2019-01-31 18:46:43 -05:00
Axel Kohlmeyer 763dda64af update lib/gpu/README to current state 2019-01-31 18:45:17 -05:00
Axel Kohlmeyer 1465352454 some cleanups and small bugfixes to conform better with python conventions 2019-01-28 17:37:05 -05:00
Axel Kohlmeyer 0cae619320 increase portability by using python modules instead of subprocesses 2019-01-28 15:54:19 -05:00
Axel Kohlmeyer b7ab017a76 improve portability by using shutil.copyfile, os.path.join, and make -C 2019-01-28 17:44:46 +01:00
Axel Kohlmeyer 4fcfa4987a fix typo 2019-01-28 14:56:47 +01:00
Axel Kohlmeyer 53f600ea35 use enable all available plumed modules when using download/compile mode 2019-01-26 09:55:48 -05:00
Axel Kohlmeyer 53673cd99c fix typo 2019-01-20 16:01:34 -05:00
Ryan S. Elliott 23ce00f366 Merge remote-tracking branch 'lammps/master' into kim-v2-update 2019-01-16 21:49:14 -06:00
Axel Kohlmeyer 683f8854c2 a few more Install.py script changes. untested. 2019-01-15 23:02:49 -05:00
Axel Kohlmeyer f8a8704ef4 use os.path.join(), os.symlink(), shutile.copyfile() and tarfile module 2019-01-15 18:07:50 -05:00
Axel Kohlmeyer 1ae112e563 small tweaks and improved consistency for Install.py in lib/kim 2019-01-14 18:03:32 -05:00
Axel Kohlmeyer cea0855fe4 small programming style cleanup 2019-01-14 17:47:58 -05:00
Axel Kohlmeyer d01c28002f update plumed support to use newer version of the library 2019-01-14 17:47:36 -05:00
Axel Kohlmeyer 54679b69f4 add argparse support to Install.py for kim library 2019-01-14 17:40:18 -05:00
Axel Kohlmeyer dc5385b290 add argparse support to Install.py in message lib 2019-01-14 17:13:46 -05:00
Axel Kohlmeyer 659bec582e update Install.py for LATTE to use the argparse module 2019-01-14 16:54:44 -05:00
Axel Kohlmeyer 2604b60eb8 properly apply version flag 2019-01-14 16:29:07 -05:00
Axel Kohlmeyer 718428df68 add md5 sum check for Voro++ download via Install.py 2019-01-14 15:03:29 -05:00
Axel Kohlmeyer 4eb141391b add md5 sum check for Eigen3 download via Install.py 2019-01-14 15:03:07 -05:00
Axel Kohlmeyer 23ad82a074 add md5sum check for ScaFaCoS download via Install.py 2019-01-14 15:02:38 -05:00
Axel Kohlmeyer ef25afcedb update Install.py for ScaFaCoS to use argparse 2019-01-14 14:44:32 -05:00
Axel Kohlmeyer e4cf409d69 update default Eigen3 version to the latest release 2019-01-14 14:13:53 -05:00
Axel Kohlmeyer c3a15e221d use sys.exit() instead of the removed error() function 2019-01-14 14:13:40 -05:00
Axel Kohlmeyer 59559f74e6 make smd/Eigen library Install.py script use argparse module 2019-01-14 13:55:22 -05:00
Axel Kohlmeyer 1e1f754d0c make gpu library Install.py use argparse module 2019-01-14 12:52:21 -05:00
Axel Kohlmeyer 8d4bfa1aa7 port plumed and mscg Install.py files to use argparse 2019-01-14 12:52:21 -05:00
Axel Kohlmeyer 3aacea671e use argparse in colvars lib build 2019-01-14 12:52:21 -05:00
Axel Kohlmeyer 4e7329151d update generic Install.py script to use argparse 2019-01-14 12:52:21 -05:00
Axel Kohlmeyer aad8dd1462 use argparse for more consistent and robust argument parsing. 
this uses the code in PR #1244 as template. it supersedes the PR and thus closes #1244
 2019-01-14 12:52:21 -05:00
Ryan S. Elliott 6c0b100a53 Merge branch 'master' into kim-v2-update 2018-12-16 15:56:33 -06:00
Ryan S. Elliott b068690e13 Update for kim-api beta.3 release 2018-12-12 16:21:54 -06:00
Axel Kohlmeyer 02bdda0d05 Merge branch 'remove-reax-meam' into collected-post-stable-patches 2018-12-12 00:14:58 -05:00
Axel Kohlmeyer 0a610cb482 Merge branch 'sllod' into collected-post-stable-patches 2018-12-12 00:14:33 -05:00
Axel Kohlmeyer d15e4b1546
Merge branch 'master' into remove-reax-meam 2018-12-11 23:31:48 -05:00
Axel Kohlmeyer 8b5887bfb1 remove MEAM and REAX from lib folder 2018-12-10 12:05:29 -05:00
Axel Kohlmeyer fb08d3ea46 ignore MSCG build folder more generally 2018-12-10 11:25:24 -05:00
Axel Kohlmeyer 45b6b4bf52 Merge branch 'python-script-portability' into collected-post-stable-patches 2018-12-03 19:47:37 -05:00