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chrissweet avatar izaguirr avatar jcoffland avatar omegaice avatar rampantmonkey avatar rnowling avatar

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omegaice siyorliang zuoyanizz np-prob rnowling

protomol's Issues

Time based configuration

Currently the total simulation time and output are defined as a number of steps which gets affected by the timestep of the top level Integrator. It would be nice to have the option of specifying these parameters with time units instead and have them be auto calculated based on the integrator.

Parallel testing with TravisCI

Currently, the TravisCI script builds and tests the serial version of ProtoMol. It would be useful to extend it to build the parallel version and then run the tests in parallel as well.

Add configuration options for DCD Caching

DCD Caching was added in 205896f to reduce the I/O hit of running many simulations at once. Currently it is defaulted off but a configuration option should be added to allow for tuning of it per simulation.

Missing input TPR causes segfault 

#0  0x00007fff98810414 in strrchr () from /usr/lib/system/libsystem_c.dylib
#1  0x000000010107182e in ShortProgram () from /usr/local/lib/libgmx.8.dylib
#2  0x0000000101043ed7 in _gmx_error () from /usr/local/lib/libgmx.8.dylib
#3  0x0000000101047f4a in gmx_fio_open () from /usr/local/lib/libgmx.8.dylib
#4  0x0000000101076b91 in read_tpxheader () from /usr/local/lib/libgmx.8.dylib
#5  0x000000010044afac in ProtoMol::buildTopologyFromTpr (topo=0x1016116d0, pos=..., vel=..., fname=..., newpositions=false, newvelocities=false) at /Users/Omegaice/Documents/Code/ProtoMol/protomol/topology/BuildTopologyFromTpr.cpp:206
#6  0x00000001000092b1 in ProtoMol::ProtoMolApp::build (this=0x7fff5fbfecb0) at /Users/Omegaice/Documents/Code/ProtoMol/protomol/ProtoMolApp.cpp:307
#7  0x0000000100002484 in main (argc=2, argv=0x7fff5fbff758) at /Users/Omegaice/Documents/Code/ProtoMol/protomol/main.cpp:21

Clang Compilation

Code currently wont compile on OS X with Clang due to debugging code.

Rare Bug: MaxEigenvalue Write for HessianInt

With current master (63480a7) running the following test produces an error very rarely. It is an error in the outputted eigenvector file and the max_eigenvalue is incorrect.

python test.py -t tests/wwdomain_CHARMM_VACUUM_HESSIAN.conf --verbose

Expected: 0.000000, Actual: -14.455000, Difference: 14.455000

Built on OS X with GCC 4.9.1 and standard lapack.

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