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‎docs/src/software/i-pi.sec‎

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@@ -13,3 +13,4 @@ it on the `ipi-code website <http://ipi-code.org>`_, the `documentation pages
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- examples/pi-metad/pi-metad
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- examples/heat-capacity/heat-capacity
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- examples/pi-mts-rpc/mts-rpc
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- examples/free-energy/free-energy

‎docs/src/topics/analysis.sec‎

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@@ -7,3 +7,4 @@ for analysis or visualization purposes.
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- examples/gaas-map/gaas-map
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- examples/lpr/lpr
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- examples/roy-gch/roy-gch
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- examples/free-energy/free-energy

‎examples/free-energy/README.rst‎

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Free energy methods
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===================

‎examples/free-energy/data.zip‎

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‎examples/free-energy/data/FES-md_hiq.bz2‎

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‎examples/free-energy/data/FES-pimd_hiq.bz2‎

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‎examples/free-energy/data/h5o2+.xyz‎

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# CELL(abcABC): 13.38377 13.38377 13.38377 90.00000 90.00000 90.00000 cell{angstrom} Traj: positions{angstrom} Step: 0 Bead: 10
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O 5.40450e-01 -9.74850e-01 -2.16580e-01
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O 2.92484e+00 -8.39252e-01 1.52397e-01
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H 1.83860e-01 -1.25804e+00 -1.07875e+00
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H 1.74329e+00 -9.09278e-01 -1.00395e-01
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H 3.29707e+00 -1.59324e+00 6.47253e-01
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H 3.53033e+00 -6.08138e-01 -5.76078e-01
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H 4.23316e-02 -1.94860e-01 9.22810e-02

‎examples/free-energy/data/h5o2.dms4B.coeff.com.dat‎

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‎examples/free-energy/data/h5o2.pes4B.coeff.dat‎

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‎examples/free-energy/data/input-md.xml‎

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<simulation safe_stride='10' verbosity='medium'>
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<ffsocket mode='unix' name='driver'>
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<latency> 1.00000000e-04</latency> <address>zundel</address>
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</ffsocket>
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<ffplumed name="plumed">
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<file mode="xyz">data/h5o2+.xyz</file>
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<plumeddat> data/plumed-md.dat </plumeddat>
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<plumed_extras> [doo, co1.lessthan, co2.lessthan, dc, mtd.bias ] </plumed_extras>
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</ffplumed>
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<total_steps>5000</total_steps>
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<output prefix="meta-md">
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<trajectory stride="10" filename="pos" cell_units="angstrom">positions{angstrom}</trajectory>
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<trajectory stride="10" filename="colvar" bead="0" extra_type="doo,dc,mtd.bias"> extras_bias </trajectory>
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<properties stride="10">
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[ step, time, conserved, temperature{kelvin}, kinetic_md,
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potential, temperature{kelvin}(H), temperature{kelvin}(O), ensemble_bias ]
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</properties>
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</output>
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<prng>
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<seed>18885</seed>
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</prng>
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<system>
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<forces>
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<force forcefield="driver"></force>
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</forces>
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<initialize nbeads="1">
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<file mode="xyz">data/h5o2+.xyz</file>
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<cell>
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[ 25.29166, 0, 0, 0, 25.29166, 0, 0, 0, 25.29166 ]
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</cell>
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</initialize>
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<ensemble>
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<temperature units="kelvin"> 300.0 </temperature>
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<bias>
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<force forcefield="plumed"/>
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</bias>
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</ensemble>
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<motion mode="dynamics">
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<fixcom> False </fixcom>
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<dynamics mode="nvt" splitting="baoab">
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<timestep units="femtosecond"> 1.0 </timestep>
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<!--
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# Generated at http://cosmo-epfl.github.io/gle4md
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# Please cite:
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# M. Ceriotti, G. Bussi and M. Parrinello, J. Chem. Theory Comput. 6, 1170 (2010)
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# M. Ceriotti, G. Bussi and M. Parrinello, Phys. Rev. Lett. 102, 020601 (2009)
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# Smart-sampling GLE. Enforces efficient sampling, focussing the effort on the slowest mode
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# accessible by the simulation. Generated from the parameter file
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# library/smart/smart-0.5_6-2.a,
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# and shifted so that they are effective to sample optimally
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# a time scale of t_opt=1 picoseconds,
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# and do as well as possible upt to a cutoff frequency of
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# νmax=100 THz [3336 cm^-1]
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-->
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<thermostat mode='gle'>
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<A shape='(7,7)'>
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[ 8.191023526179e-4, 8.328506066524e-3, 1.657771834013e-3, 9.736989925341e-4, 2.841803794895e-4, -3.176846864198e-5, -2.967010478210e-4,
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-8.389856546341e-4, 2.405526974742e-2, -1.507872374848e-2, 2.589784240185e-3, 1.516783633362e-3, -5.958833418565e-4, 4.198422349789e-4,
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7.798710586406e-4, 1.507872374848e-2, 8.569039501219e-3, 6.001000899602e-3, 1.062029383877e-3, 1.093939147968e-3, -2.661575532976e-3,
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-9.676783161546e-4, -2.589784240185e-3, -6.001000899602e-3, 2.680459336535e-5, -5.214694469742e-5, 4.231304910751e-4, -2.104894919743e-5,
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-2.841997149166e-4, -1.516783633362e-3, -1.062029383877e-3, 5.214694469742e-5, 1.433903506353e-9, -4.241574212449e-5, 7.910178912362e-5,
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3.333208286893e-5, 5.958833418565e-4, -1.093939147968e-3, -4.231304910751e-4, 4.241574212449e-5, 2.385554468441e-8, -3.139255482869e-5,
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2.967533789056e-4, -4.198422349789e-4, 2.661575532976e-3, 2.104894919743e-5, -7.910178912362e-5, 3.139255482869e-5, 2.432567259684e-11
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]
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</A>
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</thermostat>
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</dynamics>
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</motion>
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</system>
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<smotion mode="metad">
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<metad> <metaff> [ plumed ] </metaff> </metad>
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</smotion>
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</simulation>

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