Bug and Compatibility Fix

[LouYu2015]

This pull request addresses the following issues:

• 99ec9f4: When generating stiffness matrix, an underscore in a folder name will result in a wrong data file name. This should solve execution error #51
• a1b559b: Since version 1.16.3, NumPy requires explicitly allowing pickle due to security concerns.
• 0ce91c0: When parsing a configuration file, a line with only plain numbers was inteperated as a floating point array (e.g. 1; 3; 8). However, PASV_ELEM and ACTV_ELEM need to be integer array. I added a dtype parameter to _tpd2vec, forcing type conversion.

I didn't do an extensive testing. I tried the t-piece example and no regression is found.

[williamhunter]

Thanks!