diff --git a/docs/src/features.rst b/docs/src/features.rst index 4b23ebc6c..8cdd67380 100644 --- a/docs/src/features.rst +++ b/docs/src/features.rst @@ -94,13 +94,13 @@ falls back to a safe baseline potential when the ML models fail. | G. Imbalzano, Y. Zhuang, V. Kapil, K. Rossi, E. A. Engel, F. Grasselli, and M. Ceriotti, *“Uncertainty estimation for molecular dynamics and sampling”*, J. Chem. Phys. 154(7), 074102 (2021) -| DOI: `10.1063/5.0036522 `__ — BibTeX: +| DOI: `10.1063/5.0036522 `__ — BibTeX: `fetch `__ | F. Musil, M. J. Willatt, M. A. Langovoy, and M. Ceriotti, *“Fast and Accurate Uncertainty Estimation in Chemical Machine Learning”*, Journal of Chemical Theory and Computation 15(2), 906–915 (2019) | DOI: - `10.1021/acs.jctc.8b00959 `__ — + `10.1021/acs.jctc.8b00959 `__ — BibTeX: `fetch `__ @@ -132,7 +132,7 @@ direction. | **Implementation and Theory:** | M. Hijazi, D. M. Wilkins, *“Fast-forward Langevin dynamics with momentum flips”*, J. Chem. Phys. 148, 184109 (2018) -| DOI: `10.1063/1.5029833 `__ — BibTeX: +| DOI: `10.1063/1.5029833 `__ — BibTeX: `fetch `__ @@ -183,7 +183,7 @@ the harmonic Hessian. Fluctuations in Molecular Crystals: A First-Principles Study of the Stability of Paracetamol”*, Phs. Rev. Lett. 117, 115702 (2016) | DOI: - `10.1103/PhysRevLett.117.115702 `__ + `10.1103/PhysRevLett.117.115702 `__ — BibTeX: `fetch `__ @@ -204,7 +204,7 @@ other masses. | Michele Ceriotti, Thomas E. Markland, “Efficient methods and practical guidelines for simulating isotope effects.” The Journal of chemical physics 138(1), 014112 (2013). -| DOI: `10.1063/1.4772676 `__ — BibTeX: +| DOI: `10.1063/1.4772676 `__ — BibTeX: `fetch `__ Generalized Langevin Equation Thermostats @@ -296,21 +296,21 @@ adjust the amount of compensation automatically. Accurate Car-Parrinello-like Approach to Born-Oppenheimer Molecular Dynamics”*, Phys. Rev. Lett. 98, 066401 (2007) | DOI: - `10.1103/PhysRevLett.98.066401 `__ + `10.1103/PhysRevLett.98.066401 `__ — BibTeX: `fetch `__ | F. R. Krajewski, M. Parrinello, *“Linear scaling electronic structure calculations and accurate statistical mechanics sampling with noisy forces”*, Phys. Rev. B 73, 041105 (2006) | DOI: - `10.1103/PhysRevB.73.041105 `__ + `10.1103/PhysRevB.73.041105 `__ — BibTeX: `fetch `__ | Y. Luo, A. Zen, S. Sorella, *“Ab initio molecular dynamics with noisy forces: Validating the quantum Monte Carlo approach with benchmark calculations of molecular vibrational properties”*, J. Chem. Phys. 141, 194112 (2014) -| DOI: `10.1063/1.4901430 `__ — BibTeX: +| DOI: `10.1063/1.4901430 `__ — BibTeX: `fetch `__ Multiple Time Step integrators @@ -350,7 +350,7 @@ fluctuations of nuclei. Momentum Distribution in Water”*, J. Phys. Chem. B 122, 6048-6054 (2018) | DOI: - `10.1021/acs.jpcb.8b03896 `__ — + `10.1021/acs.jpcb.8b03896 `__ — BibTeX: `fetch `__ | **Theory:** @@ -493,20 +493,20 @@ of configurations between parallel calculations. Ceriotti, C. Corminboeuf, *“Beyond static structures: Putting forth remd as a tool to solve problems in computational organic chemistry”*, J. Comput. Chem. 37(1), 83-92 (2016) -| DOI: `10.1002/jcc.24025 `__ — BibTeX: +| DOI: `10.1002/jcc.24025 `__ — BibTeX: `fetch `__ | **Theory:** | Y. Sugita, Y. Okamoto, *“Replica-exchange molecular dynamics method for protein folding”*, Chem. Phys. Lett. 314(1-2), 141–151 (1999) | DOI: - `10.1016/s0009-2614(99)01123-9 `__ + `10.1016/s0009-2614(99)01123-9 `__ — BibTeX: `fetch `__ | T. Okabe, M. Kawata, Y. Okamoto, M. Mikami, *“Replica-exchange monte carlo method for the isobaric–isothermal ensemble”*, Chem. Phys. Lett. 335(5-6), 435-439 (2001) | DOI: `10.1016/ - s0009-2614(01)00055-0 `__ — + s0009-2614(01)00055-0 `__ — BibTeX: `fetch `__ @@ -522,7 +522,7 @@ species into its isotopes. Effects in Water at the Triple Point: Using Theory as a Link Between Experiments.”* J. Phys. Chem. Lett. 7(12), 2210-2215 (2016) | DOI: - `10.1021/acs.jpclett.6b00729 `__ + `10.1021/acs.jpclett.6b00729 `__ — BibTeX: `fetch `__ | **Theory:** @@ -624,13 +624,13 @@ coordinate. | W. H. Miller, *Semiclassical limit of quantum mechanical transition state theory for nonseparable systems*, J. Chem. Phys. 62(5) 1899–1906 (1975) -| DOI: `10.1063/1.430676 `__ — BibTeX: - `fetch `__ +| DOI: `10.1063/1.430676 `__ — BibTeX: + `fetch `__ | J. O. Richardson, *Ring-polymer instanton theory*, Int. Rev. Phys. Chem. 37, 171 (2018) | DOI: - `10.1080/0144235X.2018.1472353 `__ - — BibTeX: `fetch `__ + `10.1080/0144235X.2018.1472353 `__ + — BibTeX: `fetch `__ Thermodynamic Integrations -------------------------- diff --git a/docs/src/getting-started.rst b/docs/src/getting-started.rst index 54b587657..fcc32010e 100644 --- a/docs/src/getting-started.rst +++ b/docs/src/getting-started.rst @@ -312,7 +312,8 @@ modification is necessary: &END MOTION The rest of the input file should be the same as for a standard CP2K -calculation, as explained at `www.cp2k.org/ `__. +calculation, as explained at it the documentation of +`CP2K `__. Quantum-Espresso ^^^^^^^^^^^^^^^^ diff --git a/docs/src/input-files.rst b/docs/src/input-files.rst index b74a9891b..9810f580b 100644 --- a/docs/src/input-files.rst +++ b/docs/src/input-files.rst @@ -83,7 +83,7 @@ To help detect any user error the recognized tag names, data types and acceptable options are all specified in the code in a specialized input class for each class of object. A full list of all the available tags and a brief description of their function is given at -`input tags `_. +`input tags `_. .. _inputunits: diff --git a/docs/src/onlinereso.rst b/docs/src/onlinereso.rst index b25cf4b41..a5970a144 100644 --- a/docs/src/onlinereso.rst +++ b/docs/src/onlinereso.rst @@ -21,10 +21,10 @@ Python resources ~~~~~~~~~~~~~~~~ For help with Python programming, see -`www.python.org `__. For information about the NumPy -mathematical library, see `www.numpy.org `__, and for +`www.python.org `__. For information about the NumPy +mathematical library, see `www.numpy.org `__, and for worked examples of its capabilities see -`www.scipy.org/Tentative_NumPy_Tutorial `__. +`www.scipy.org/Tentative_NumPy_Tutorial `__. Finally, see http://hgomersall.github.io/pyFFTW/ for documentation on the Python FFTW library that is currently implemented with i-PI. @@ -51,9 +51,9 @@ touch, we are always glad to help! There are several Fortran and C libraries that most client codes will probably need to run, such as FFTW, BLAS and LAPACK. These can be found -at `www.fftw.org `__, -`www.netlib.org/blas `__ and -`www.netlib.org/lapack `__ respectively. +at `www.fftw.org `__, +`www.netlib.org/blas `__ and +`www.netlib.org/lapack `__ respectively. These codes do not come as part of the i-PI package, and must be downloaded separately.