Macroscopic quantities
When the PumMa version with macroscopic quantity collection is used, the code has an extra output file, which name is set by the mqfile option in the input options file. By default the name of this file is mq.pof. For every atom type nine macroscopic quantities are collected during the simulation. Look in the input option section for details on the options that can be set, prior to the simulation.
For example, if the macroscopic quantities for a system consisting of only one atom type would be collected, an excerpt of the mq.pof file could look like
... 29.7683 1.4339 1.0019 0.0008 0.0008 -0.0002 -0.0018 0.8893 0.8899 -0.9603 29.7834 1.5100 1.0003 -0.0016 0.0016 -0.0040 -0.0016 0.9637 0.9555 -0.5267 29.7985 1.5815 0.9984 -0.0131 0.0011 -0.0006 -0.0012 1.0246 1.0275 -0.0388 29.8137 1.6416 0.9985 0.0033 0.0008 0.0005 -0.0009 1.1273 1.1307 0.5417 29.8288 1.6804 1.0004 0.0037 0.0017 0.0046 -0.0005 1.2528 1.2600 1.1665 29.8439 1.7034 1.0010 0.0006 0.0003 0.0050 -0.0000 1.3942 1.4007 1.8430 29.8590 1.6967 1.0020 -0.0114 -0.0003 0.0055 0.0004 1.5477 1.5540 2.5190 29.8742 1.6679 1.0013 0.0038 0.0022 0.0034 0.0010 1.7121 1.7208 3.1569 29.8893 1.6179 1.0018 0.0221 0.0011 0.0022 0.0014 1.8804 1.8843 3.7510 29.9044 1.5447 1.0011 0.0286 0.0010 -0.0007 0.0018 2.0523 2.0777 4.2385 29.9196 1.4545 0.9989 0.0458 0.0005 -0.0008 0.0026 2.2229 2.2215 4.5968 ...
The first column are the numbers of the bins along the axis at which the data collection takes place. The next column gives the local particle number density (in nm-3), the third column the local temperature (in K) and the fourth column the local heat flux (in J/nm2/ps). The next three columns are the local average velocities in x-, y- and z-direction (in nm/ps). The last three columns give the diagonal components of the local pressure tensor (in bar).
If more than one atom type are present in the simulation, the nine macroscopic quantities are repeated columnwise on the same row. Hence, with two atom types the total number of columns is 19, where the first column contains the coordinates, the first nine columns the quantities of the first atom type, and the last nine columns the quantities of the second atom type. The order of atom types depends on the order they are being parsed initially by the simulator.
For instance, our lipid bilayer simulations contain three atom types: head, tail and water particles. The macroscopic quantity file therefore has 28 columns. If the local particle number densities are plotted against the coordinate (the second, eleventh and twentieth columns plotted against the first column), the density profile shown below could be obtained.
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