Flexible and modular virtual scanning probe microscope
Non-contact Atomic Force Microscopy (NC-AFM) is an experimental technique capable of imaging almost any surface with atomic resolution, in a wide variety of environments. Linking measured images to real understanding of system properties is often difficult, and many studies combine experiments with...
Gespeichert in:
| Veröffentlicht in: | Computer physics communications Jg. 196; S. 429 - 438 |
|---|---|
| Hauptverfasser: | , , , , , , |
| Format: | Journal Article |
| Sprache: | Englisch |
| Veröffentlicht: |
Elsevier B.V
01.11.2015
|
| Schlagworte: | |
| ISSN: | 0010-4655, 1879-2944 |
| Online-Zugang: | Volltext |
| Tags: |
Tag hinzufügen
Keine Tags, Fügen Sie den ersten Tag hinzu!
|
| Abstract | Non-contact Atomic Force Microscopy (NC-AFM) is an experimental technique capable of imaging almost any surface with atomic resolution, in a wide variety of environments. Linking measured images to real understanding of system properties is often difficult, and many studies combine experiments with detailed modelling, in particular using virtual simulators to directly mimic experimental operation. In this work we present the PyVAFM, a flexible and modular based virtual atomic force microscope capable of simulating any operational mode or set-up. Furthermore, the PyVAFM is fully expandable to allow novel and unique set-ups to be simulated, finally the PyVAFM ships with fully developed documentation and tutorial to increase usability.
Program title: Python Virtual Atomic Force Microscope (PyVAFM)
Catalogue identifier: AEWX_v1_0
Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEWX_v1_0.html
Program obtainable from: CPC Program Library, Queen’s University, Belfast, N. Ireland
Licensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.html
No. of lines in distributed program, including test data, etc.: 852449
No. of bytes in distributed program, including test data, etc.: 28531404
Distribution format:.ZIP
Programming language: Python input scripts and a C core.
Computer: Desktop.
Operating system: UNIX.
RAM: 500 Megabytes
Classification: 16.4.
External routines: GCC, Python 2.7, scipy and numpy
Nature of problem: Simulation of any atomic force microscope operational mode including experimental delays/artefacts.
Solution method: A modular simulation was developed where a user can connect several components together in order to simulate any operational mode. Each of these components is also developed to be mathematically similar to their real life counter parts hence incorporating any experimental delays or artefacts.
Restrictions: For tip-sample interactions beyond simple analytical forms, the interaction field should be provided by the user via separate simulations e.g first principles or classical calculations.
Unusual features: Modularity
Additional comments: The tutorials include several example tip-sample interaction approaches and fields, and authors can provide others upon request.
Running time: 2 h. The example given in the installation section of the user manual only takes about 30 s. |
|---|---|
| AbstractList | Non-contact Atomic Force Microscopy (NC-AFM) is an experimental technique capable of imaging almost any surface with atomic resolution, in a wide variety of environments. Linking measured images to real understanding of system properties is often difficult, and many studies combine experiments with detailed modelling, in particular using virtual simulators to directly mimic experimental operation. In this work we present the PyVAFM, a flexible and modular based virtual atomic force microscope capable of simulating any operational mode or set-up. Furthermore, the PyVAFM is fully expandable to allow novel and unique set-ups to be simulated, finally the PyVAFM ships with fully developed documentation and tutorial to increase usability. Program summary Program title: Python Virtual Atomic Force Microscope (PyVAFM) Catalogue identifier: AEWX_v1_0 Program summary URL: http://cpc.cs.qub.ac.uk/summaries/AEWX_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.html No. of lines in distributed program, including test data, etc.: 852449 No. of bytes in distributed program, including test data, etc.: 28531404 Distribution format:.ZIP Programming language: Python input scripts and a C core. Computer: Desktop. Operating system: UNIX. RAM: 500 Megabytes Classification: 16.4. External routines: GCC, Python 2.7, scipy and numpy Nature of problem: Simulation of any atomic force microscope operational mode including experimental delays/artefacts. Solution method: A modular simulation was developed where a user can connect several components together in order to simulate any operational mode. Each of these components is also developed to be mathematically similar to their real life counter parts hence incorporating any experimental delays or artefacts. Restrictions: For tip-sample interactions beyond simple analytical forms, the interaction field should be provided by the user via separate simulations e.g first principles or classical calculations. Unusual features: Modularity Additional comments: The tutorials include several example tip-sample interaction approaches and fields, and authors can provide others upon request. Running time: 2 h. The example given in the installation section of the user manual only takes about 30 s. Non-contact Atomic Force Microscopy (NC-AFM) is an experimental technique capable of imaging almost any surface with atomic resolution, in a wide variety of environments. Linking measured images to real understanding of system properties is often difficult, and many studies combine experiments with detailed modelling, in particular using virtual simulators to directly mimic experimental operation. In this work we present the PyVAFM, a flexible and modular based virtual atomic force microscope capable of simulating any operational mode or set-up. Furthermore, the PyVAFM is fully expandable to allow novel and unique set-ups to be simulated, finally the PyVAFM ships with fully developed documentation and tutorial to increase usability. Program title: Python Virtual Atomic Force Microscope (PyVAFM) Catalogue identifier: AEWX_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEWX_v1_0.html Program obtainable from: CPC Program Library, Queen’s University, Belfast, N. Ireland Licensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.html No. of lines in distributed program, including test data, etc.: 852449 No. of bytes in distributed program, including test data, etc.: 28531404 Distribution format:.ZIP Programming language: Python input scripts and a C core. Computer: Desktop. Operating system: UNIX. RAM: 500 Megabytes Classification: 16.4. External routines: GCC, Python 2.7, scipy and numpy Nature of problem: Simulation of any atomic force microscope operational mode including experimental delays/artefacts. Solution method: A modular simulation was developed where a user can connect several components together in order to simulate any operational mode. Each of these components is also developed to be mathematically similar to their real life counter parts hence incorporating any experimental delays or artefacts. Restrictions: For tip-sample interactions beyond simple analytical forms, the interaction field should be provided by the user via separate simulations e.g first principles or classical calculations. Unusual features: Modularity Additional comments: The tutorials include several example tip-sample interaction approaches and fields, and authors can provide others upon request. Running time: 2 h. The example given in the installation section of the user manual only takes about 30 s. |
| Author | Federici Canova, Filippo Gao, David Z. Tracey, John Reischl, Bernhard Spijker, Peter Keisanen, Olli Foster, Adam S. |
| Author_xml | – sequence: 1 givenname: John surname: Tracey fullname: Tracey, John email: john.tracey@aalto.fi organization: COMP, Department of Applied Physics, Aalto University, Otakaari 1, FI-00076 Aalto, Finland – sequence: 2 givenname: Filippo surname: Federici Canova fullname: Federici Canova, Filippo organization: Aalto Science Institute, Aalto School of Science, PO Box 15500, FI-00076, Aalto, Finland – sequence: 3 givenname: Olli surname: Keisanen fullname: Keisanen, Olli organization: COMP, Department of Applied Physics, Aalto University, Otakaari 1, FI-00076 Aalto, Finland – sequence: 4 givenname: David Z. surname: Gao fullname: Gao, David Z. organization: Department of Physics and Astronomy, University College London, Gower Street, London WC1E 6BT, United Kingdom – sequence: 5 givenname: Peter surname: Spijker fullname: Spijker, Peter organization: COMP, Department of Applied Physics, Aalto University, Otakaari 1, FI-00076 Aalto, Finland – sequence: 6 givenname: Bernhard surname: Reischl fullname: Reischl, Bernhard organization: Nanochemistry Research Institute, Curtin Institute for Computation, Department of Chemistry, Curtin University, GPO Box U1987, WA 6845, Perth, Australia – sequence: 7 givenname: Adam S. surname: Foster fullname: Foster, Adam S. organization: COMP, Department of Applied Physics, Aalto University, Otakaari 1, FI-00076 Aalto, Finland |
| BookMark | eNp9kDFPwzAUhC1UJNrCD2DLyJLybCdxIiZUUUCqxAKz5TjPyJXjBDup4N-TqEwMlU56y32ne7ciC995JOSWwoYCLe4PG93rDQOab2AS5RdkSUtRpazKsgVZAlBIsyLPr8gqxgMACFHxJSl2Dr9t7TBRvknarhmdCsnRhmFULolaeW_9Z9KHrsaktTp0UXc9XpNLo1zEm7-7Jh-7p_ftS7p_e37dPu5TnQEMqeDc1AVnhlKV1Xlp0OhGl5ArMBUzWVaXucg1LRsGFROshrLKDOMcFWoGnK_J3Sl3KvA1Yhxka6NG55THboySClECy0tBJys9WeeOMaCRfbCtCj-Sgpw3kgc5bSTnjSRMonO8-MdoO6jBdn4Iyrqz5MOJxOn7o8Ugo7boNTY2oB5k09kz9C9MhIJb |
| CitedBy_id | crossref_primary_10_1103_PhysRevApplied_11_024068 crossref_primary_10_1088_0957_4484_27_41_415709 crossref_primary_10_1063_1_5078954 |
| Cites_doi | 10.1088/0957-4484/23/13/135706 10.1021/nn501785q 10.1021/jp311702j 10.1103/PhysRevB.90.085421 10.1103/RevModPhys.75.949 10.1063/1.368181 10.1016/j.surfrep.2010.10.001 10.1103/PhysRevB.71.125424 10.1126/science.1176210 10.1051/epjap:2001175 10.1063/1.1841462 10.1088/0957-4484/22/4/045702 10.1002/admi.201400414 10.1016/S0968-4328(01)00026-9 10.1021/la803448v 10.1088/0957-4484/23/32/325703 10.1088/0957-4484/18/8/084017 10.1007/s003390100634 10.1016/S0167-5729(02)00077-8 10.1063/1.442716 10.1103/PhysRevB.84.115415 10.1063/1.1667267 10.1063/1.103677 10.1063/1.102985 10.1002/adma.201002270 10.1103/PhysRevB.74.235439 10.1103/PhysRevB.76.085414 10.1088/0957-4484/23/18/185306 10.1021/nl101290t 10.1103/PhysRevB.31.805 10.1103/PhysRevLett.109.146101 10.1103/RevModPhys.75.1287 10.1103/PhysRevB.59.2436 10.1103/PhysRevB.56.16010 10.1103/PhysRevB.76.245421 10.1021/ct3008342 10.1016/S0167-5729(97)80003-9 10.1103/PhysRevLett.107.036102 |
| ContentType | Journal Article |
| Copyright | 2015 Elsevier B.V. |
| Copyright_xml | – notice: 2015 Elsevier B.V. |
| DBID | AAYXX CITATION 7SC 7U5 8FD H8D JQ2 L7M L~C L~D |
| DOI | 10.1016/j.cpc.2015.05.013 |
| DatabaseName | CrossRef Computer and Information Systems Abstracts Solid State and Superconductivity Abstracts Technology Research Database Aerospace Database ProQuest Computer Science Collection Advanced Technologies Database with Aerospace Computer and Information Systems Abstracts Academic Computer and Information Systems Abstracts Professional |
| DatabaseTitle | CrossRef Aerospace Database Technology Research Database Computer and Information Systems Abstracts – Academic ProQuest Computer Science Collection Computer and Information Systems Abstracts Solid State and Superconductivity Abstracts Advanced Technologies Database with Aerospace Computer and Information Systems Abstracts Professional |
| DatabaseTitleList | Aerospace Database |
| DeliveryMethod | fulltext_linktorsrc |
| Discipline | Physics |
| EISSN | 1879-2944 |
| EndPage | 438 |
| ExternalDocumentID | 10_1016_j_cpc_2015_05_013 S0010465515001939 |
| GroupedDBID | --K --M -~X .DC .~1 0R~ 1B1 1RT 1~. 1~5 29F 4.4 457 4G. 5GY 5VS 7-5 71M 8P~ 9JN AACTN AAEDT AAEDW AAIAV AAIKJ AAKOC AALRI AAOAW AAQFI AAQXK AARLI AAXUO AAYFN ABBOA ABFNM ABMAC ABNEU ABQEM ABQYD ABXDB ABYKQ ACDAQ ACFVG ACGFS ACLVX ACNNM ACRLP ACSBN ACZNC ADBBV ADECG ADEZE ADJOM ADMUD AEBSH AEKER AENEX AFKWA AFTJW AFZHZ AGHFR AGUBO AGYEJ AHHHB AHZHX AI. AIALX AIEXJ AIKHN AITUG AIVDX AJBFU AJOXV AJSZI ALMA_UNASSIGNED_HOLDINGS AMFUW AMRAJ AOUOD ASPBG ATOGT AVWKF AXJTR AZFZN BBWZM BKOJK BLXMC CS3 DU5 EBS EFJIC EFLBG EJD EO8 EO9 EP2 EP3 F5P FDB FEDTE FGOYB FIRID FLBIZ FNPLU FYGXN G-2 G-Q GBLVA GBOLZ HLZ HME HMV HVGLF HZ~ IHE IMUCA J1W KOM LG9 LZ4 M38 M41 MO0 N9A NDZJH O-L O9- OAUVE OGIMB OZT P-8 P-9 P2P PC. Q38 R2- RIG ROL RPZ SBC SCB SDF SDG SES SEW SHN SPC SPCBC SPD SPG SSE SSK SSQ SSV SSZ T5K TN5 UPT VH1 WUQ ZMT ~02 ~G- 9DU AATTM AAXKI AAYWO AAYXX ABJNI ABWVN ACLOT ACRPL ACVFH ADCNI ADNMO AEIPS AEUPX AFJKZ AFPUW AGQPQ AIGII AIIUN AKBMS AKRWK AKYEP ANKPU APXCP CITATION EFKBS ~HD 7SC 7U5 8FD H8D JQ2 L7M L~C L~D |
| ID | FETCH-LOGICAL-c400t-733fb632f11a4b58fefcdc805a0f92f44b8575c18d209272b0894f233eaec2033 |
| ISICitedReferencesCount | 8 |
| ISICitedReferencesURI | http://www.webofscience.com/api/gateway?GWVersion=2&SrcApp=Summon&SrcAuth=ProQuest&DestLinkType=CitingArticles&DestApp=WOS_CPL&KeyUT=000362602900040&url=https%3A%2F%2Fcvtisr.summon.serialssolutions.com%2F%23%21%2Fsearch%3Fho%3Df%26include.ft.matches%3Dt%26l%3Dnull%26q%3D |
| ISSN | 0010-4655 |
| IngestDate | Sun Sep 28 10:29:38 EDT 2025 Sat Nov 29 07:32:11 EST 2025 Tue Nov 18 22:33:28 EST 2025 Fri Feb 23 02:30:58 EST 2024 |
| IsPeerReviewed | true |
| IsScholarly | true |
| Keywords | SPM Simulation NC-AFM Python |
| Language | English |
| LinkModel | OpenURL |
| MergedId | FETCHMERGED-LOGICAL-c400t-733fb632f11a4b58fefcdc805a0f92f44b8575c18d209272b0894f233eaec2033 |
| Notes | ObjectType-Article-1 SourceType-Scholarly Journals-1 ObjectType-Feature-2 content type line 23 |
| PQID | 1778025871 |
| PQPubID | 23500 |
| PageCount | 10 |
| ParticipantIDs | proquest_miscellaneous_1778025871 crossref_primary_10_1016_j_cpc_2015_05_013 crossref_citationtrail_10_1016_j_cpc_2015_05_013 elsevier_sciencedirect_doi_10_1016_j_cpc_2015_05_013 |
| PublicationCentury | 2000 |
| PublicationDate | 2015-11-01 |
| PublicationDateYYYYMMDD | 2015-11-01 |
| PublicationDate_xml | – month: 11 year: 2015 text: 2015-11-01 day: 01 |
| PublicationDecade | 2010 |
| PublicationTitle | Computer physics communications |
| PublicationYear | 2015 |
| Publisher | Elsevier B.V |
| Publisher_xml | – name: Elsevier B.V |
| References | Barth, Foster, Henry, Shluger (br000055) 2011; 23 Schwarz, Gao, Lämmle, Grenz, Watkins, Shluger, Wiesendanger (br000025) 2013; 117 Akamine, Barrett, Quate (br000135) 1990; 57 Trevethan, Kantorovich, Polesel-Maris, Gauthier (br000105) 2007; 18 Trevethan, Kantorovich, Polesel-Maris, Gauthier, Shluger (br000100) 2007; 76 (br000005) 2002 Couturier, Aim~’e, Salardenne, Boisgard (br000080) 2001; 15 Kawai, Canova, Glatzel, Hynninen, Meyer, Foster (br000115) 2012; 109 Meyer, Amer (br000015) 1990; 56 Giessibl (br000010) 2003; 75 Nony, Baratoff, Schär, Pfeiffer, Wetzel, Meyer (br000090) 2006; 74 Rode, Oyabu, Kobayashi, Yamada, Kühnle (br000155) 2009; 25 Ikai (br000030) 1996; 26 Amrous, Bocquet, Nony, Para, Loppacher, Lamare, Palmino, Cherioux, Gao, Federici Canova, Watkins, Shluger (br000125) 2014; 1 Melitz, Shen, Kummel, Lee (br000190) 2010; 66 Couturier, Aime, Salardenne, Boisgard, Gourdon, Gauthier (br000075) 2001; 72 Gao, Grenz, Watkins, Federici~Canova, Schwarz, Wiesendanger, Shluger (br000165) 2014; 8 Rasmussen, Foster, Hinnemann, Canova, Helveg, Meinander, Martin, Knudsen, Vlad, Lundgren, Stierle, Besenbacher, Lauritsen (br000120) 2011; 107 Watkins, Trevethan, Shluger, Kantorovich (br000095) 2007; 76 Federici~Canova, Foster (br000200) 2011; 22 García, Pérez (br000045) 2002; 47 Argento, French (br000160) 1996; 80 Swope, Andersen, Berens, Wilson (br000130) 1982; 76 Clark, Qin, Zhang, Li (br000140) 2012; 23 Reischl, Watkins, Foster (br000150) 2013; 9 Zerweck, Loppacher, Otto, Grafström, Eng (br000185) 2005; 71 Tersoff, Hamann (br000195) 1985; 31 Lämmle, Trevethan, Schwarz, Watkins, Shluger, Wiesendanger (br000020) 2010; 10 Hofer, Foster, Shluger (br000050) 2003; 75 Sader, Jarvis (br000070) 2004; 84 Gross, Mohn, Moll, Liljeroth, Meyer (br000170) 2009; 325 Fotiadis, Scheuring, Müller, Engel, Müller (br000035) 2002; 33 Kawai, Canova, Glatzel, Foster, Meyer (br000145) 2011; 84 Livshits, Shluger, Rohl, Foster (br000065) 1999; 59 Federici Canova, Foster, Rasmussen, Meinander, Besenbacher, Lauritsen (br000110) 2012; 23 Polesel-Maris, Gauthier (br000085) 2005; 97 Giessibl (br000060) 1997; 56 Hapala, Kichin, Wagner, Tautz, Temirov, Jelinek (br000175) 2014; 90 Fukuma, Onishi, Kobayashi, Matsuki, Asakawa (br000040) 2012; 23 Jacobs, Leuchtmann, Homan, Stemmer (br000180) 1998; 84 Schwarz (10.1016/j.cpc.2015.05.013_br000025) 2013; 117 Lämmle (10.1016/j.cpc.2015.05.013_br000020) 2010; 10 Kawai (10.1016/j.cpc.2015.05.013_br000145) 2011; 84 Melitz (10.1016/j.cpc.2015.05.013_br000190) 2010; 66 Nony (10.1016/j.cpc.2015.05.013_br000090) 2006; 74 Federici Canova (10.1016/j.cpc.2015.05.013_br000110) 2012; 23 Couturier (10.1016/j.cpc.2015.05.013_br000080) 2001; 15 Zerweck (10.1016/j.cpc.2015.05.013_br000185) 2005; 71 Hapala (10.1016/j.cpc.2015.05.013_br000175) 2014; 90 Meyer (10.1016/j.cpc.2015.05.013_br000015) 1990; 56 Fotiadis (10.1016/j.cpc.2015.05.013_br000035) 2002; 33 Livshits (10.1016/j.cpc.2015.05.013_br000065) 1999; 59 Gao (10.1016/j.cpc.2015.05.013_br000165) 2014; 8 Tersoff (10.1016/j.cpc.2015.05.013_br000195) 1985; 31 Sader (10.1016/j.cpc.2015.05.013_br000070) 2004; 84 Swope (10.1016/j.cpc.2015.05.013_br000130) 1982; 76 Federici~Canova (10.1016/j.cpc.2015.05.013_br000200) 2011; 22 Reischl (10.1016/j.cpc.2015.05.013_br000150) 2013; 9 Rasmussen (10.1016/j.cpc.2015.05.013_br000120) 2011; 107 Rode (10.1016/j.cpc.2015.05.013_br000155) 2009; 25 Giessibl (10.1016/j.cpc.2015.05.013_br000010) 2003; 75 Ikai (10.1016/j.cpc.2015.05.013_br000030) 1996; 26 Clark (10.1016/j.cpc.2015.05.013_br000140) 2012; 23 Argento (10.1016/j.cpc.2015.05.013_br000160) 1996; 80 Trevethan (10.1016/j.cpc.2015.05.013_br000100) 2007; 76 Amrous (10.1016/j.cpc.2015.05.013_br000125) 2014; 1 Couturier (10.1016/j.cpc.2015.05.013_br000075) 2001; 72 Fukuma (10.1016/j.cpc.2015.05.013_br000040) 2012; 23 García (10.1016/j.cpc.2015.05.013_br000045) 2002; 47 Polesel-Maris (10.1016/j.cpc.2015.05.013_br000085) 2005; 97 Hofer (10.1016/j.cpc.2015.05.013_br000050) 2003; 75 Akamine (10.1016/j.cpc.2015.05.013_br000135) 1990; 57 Watkins (10.1016/j.cpc.2015.05.013_br000095) 2007; 76 Kawai (10.1016/j.cpc.2015.05.013_br000115) 2012; 109 (10.1016/j.cpc.2015.05.013_br000005) 2002 Jacobs (10.1016/j.cpc.2015.05.013_br000180) 1998; 84 Trevethan (10.1016/j.cpc.2015.05.013_br000105) 2007; 18 Giessibl (10.1016/j.cpc.2015.05.013_br000060) 1997; 56 Barth (10.1016/j.cpc.2015.05.013_br000055) 2011; 23 Gross (10.1016/j.cpc.2015.05.013_br000170) 2009; 325 |
| References_xml | – volume: 25 start-page: 2850 year: 2009 end-page: 2853 ident: br000155 article-title: True atomic-resolution imaging of (1014) Calcite in Aqueous solution by frequency modulation atomic force microscopy publication-title: Langmuir – volume: 23 start-page: 135706 year: 2012 ident: br000040 article-title: Atomic-resolution imaging in liquid by frequency modulation atomic force microscopy using small cantilevers with megahertz-order resonance frequencies publication-title: Nanotechnology – volume: 1 start-page: 2196 year: 2014 end-page: 7350 ident: br000125 article-title: Molecular design and control over the morphology of self-assembled films on ionic substrates publication-title: Adv. Mater. Interfaces – volume: 325 start-page: 1110 year: 2009 end-page: 1114 ident: br000170 article-title: The chemical structure of a molecule resolved by atomic force microscopy publication-title: Science – volume: 75 start-page: 949 year: 2003 ident: br000010 article-title: Advances in atomic force microscopy publication-title: Rev. Modern Phys. – volume: 33 start-page: 385 year: 2002 end-page: 397 ident: br000035 article-title: Imaging and manipulation of biological structures with the afm publication-title: Micron – volume: 57 start-page: 316 year: 1990 end-page: 318 ident: br000135 article-title: Improved atomic force microscope images using microcantilevers with sharp tips publication-title: Appl. Phys. Lett. – volume: 26 start-page: 261 year: 1996 end-page: 332 ident: br000030 article-title: STM and AFM of bio/organic molecules and structures publication-title: Surf. Sci. Rep. – volume: 76 start-page: 637 year: 1982 end-page: 649 ident: br000130 article-title: A computer simulation method for the calculation of equilibrium constants for the formation of physical clusters of molecules: Application to small water clusters publication-title: J. Chem. Phys. – year: 2002 ident: br000005 publication-title: Noncontact Atomic Force Microscopy – volume: 10 start-page: 2965 year: 2010 ident: br000020 article-title: Unambiguous determination of the adsorption geometry of a metal–organic complex on a bulk insulator publication-title: Nano Lett. – volume: 71 start-page: 125424 year: 2005 ident: br000185 article-title: Accuracy and resolution limits of kelvin probe force microscopy publication-title: Phys. Rev. B – volume: 84 start-page: 1168 year: 1998 end-page: 1173 ident: br000180 article-title: Resolution and contrast in Kelvin probe force microscopy publication-title: J. Appl. Phys. – volume: 56 start-page: 16010 year: 1997 ident: br000060 article-title: Forces and frequency shifts in atomic-resolution dynamic-force microscopy publication-title: Phys. Rev. B – volume: 72 start-page: S47 year: 2001 end-page: S50 ident: br000075 article-title: A mechanical approach to the dissipation process in NC-AFM: experiments, model and simulation publication-title: Appl. Phys. Mater. Sci. Process. – volume: 76 start-page: 245421 year: 2007 ident: br000095 article-title: Dynamical processes at oxide surfaces studied with the virtual atomic force microscope publication-title: Phys. Rev. B – volume: 75 start-page: 1287 year: 2003 end-page: 1331 ident: br000050 article-title: Theories of scanning probe microscopes at the atomic scale publication-title: Rev. Modern Phys. – volume: 107 start-page: 036102 year: 2011 ident: br000120 article-title: Stable cation inversion at the MgAl publication-title: Phys. Rev. Lett. – volume: 23 start-page: 477 year: 2011 end-page: 501 ident: br000055 article-title: Recent trends in surface characterization and chemistry with high-resolution scanning force methods publication-title: Adv. Mater. – volume: 74 start-page: 235439 year: 2006 ident: br000090 article-title: Noncontact atomic force microscopy simulator with phase-locked-loop controlled frequency detection and excitation publication-title: Phys. Rev. B – volume: 80 year: 1996 ident: br000160 article-title: Parametric tip model and force distance relation for hamaker constant determination from atomic force microscopy publication-title: J. Appl. Phys. – volume: 47 start-page: 197 year: 2002 ident: br000045 article-title: Dynamic atomic force microscopy methods publication-title: Surf. Sci. Rep. – volume: 15 start-page: 141 year: 2001 end-page: 147 ident: br000080 article-title: A virtual non contact-atomic force microscope (NC-AFM): Simulation and comparison with analytical models publication-title: Eur. Phys. J. Appl. Phys. – volume: 66 start-page: 1 year: 2010 end-page: 27 ident: br000190 article-title: Kelvin probe force microscopy and its application publication-title: Surf. Sci. Rep. – volume: 31 start-page: 805 year: 1985 end-page: 813 ident: br000195 article-title: Theory of the scanning tunneling microscope publication-title: Phys. Rev. B – volume: 84 start-page: 1801 year: 2004 ident: br000070 article-title: Accurate formulas for interaction force and energy in frequency modulation force spectroscopy publication-title: Appl. Phys. Lett. – volume: 76 start-page: 085414 year: 2007 ident: br000100 article-title: Multiscale model of the manipulation of single atoms on insulating surfaces using an atomic force microscope tip publication-title: Phys. Rev. B – volume: 22 start-page: 045702 year: 2011 ident: br000200 article-title: The role of the tip in non-contact atomic force microscopy dissipation images of ionic surfaces publication-title: Nanotechnology – volume: 84 start-page: 115415 year: 2011 ident: br000145 article-title: Atomic-scale dissipation processes in dynamic force spectroscopy publication-title: Phys. Rev. B – volume: 8 start-page: 5339 year: 2014 end-page: 5351 ident: br000165 article-title: Using metallic noncontact atomic force microscope tips for imaging insulators and polar molecules: tip characterization and imaging mechanisms publication-title: ACS nano – volume: 117 start-page: 1105 year: 2013 end-page: 1112 ident: br000025 article-title: Determining adsorption geometry, bonding, and translational pathways of a metal organic complex on an oxide surface: Co-salen on NiO(001) publication-title: J. Phys. Chem. C – volume: 56 start-page: 2100 year: 1990 ident: br000015 article-title: Optical-beam-deflection atomic force microscopy: The NaCl(001) surface publication-title: Appl. Phys. Lett. – volume: 97 start-page: 044902 year: 2005 ident: br000085 article-title: A virtual dynamic atomic force microscope for image calculations publication-title: J. Appl. Phys. – volume: 59 start-page: 2436 year: 1999 end-page: 2448 ident: br000065 article-title: Model of noncontact scanning force microscopy on ionic surfaces publication-title: Phys. Rev. B – volume: 9 start-page: 600 year: 2013 ident: br000150 article-title: Free energy approaches for modeling atomic force microscopy in liquids publication-title: J. Chem. Theory Comput. – volume: 90 start-page: 085421 year: 2014 ident: br000175 article-title: Mechanism of high-resolution STM/AFM imaging with functionalized tips publication-title: Phys. Rev. B – volume: 23 start-page: 185306 year: 2012 ident: br000140 article-title: Nanoscale periodic modulations on sodium chloride surface revealed by tuning fork atomic force microscopy publication-title: Nanotechnology – volume: 18 start-page: 084017 year: 2007 ident: br000105 article-title: Is atomic-scale dissipation in NC-AFM real? Investigation using virtual atomic force microscopy publication-title: Nanotechnology – volume: 23 start-page: 325703 year: 2012 ident: br000110 article-title: Non-contact atomic force microscopy study of hydroxyl groups on the spinel MgAl publication-title: Nanotechnology – volume: 109 start-page: 146101 year: 2012 ident: br000115 article-title: Measuring electric field induced subpicometer displacement of step edge ions publication-title: Phys. Rev. Lett. – volume: 23 start-page: 135706 year: 2012 ident: 10.1016/j.cpc.2015.05.013_br000040 article-title: Atomic-resolution imaging in liquid by frequency modulation atomic force microscopy using small cantilevers with megahertz-order resonance frequencies publication-title: Nanotechnology doi: 10.1088/0957-4484/23/13/135706 – volume: 8 start-page: 5339 issue: 5 year: 2014 ident: 10.1016/j.cpc.2015.05.013_br000165 article-title: Using metallic noncontact atomic force microscope tips for imaging insulators and polar molecules: tip characterization and imaging mechanisms publication-title: ACS nano doi: 10.1021/nn501785q – volume: 117 start-page: 1105 issue: 2 year: 2013 ident: 10.1016/j.cpc.2015.05.013_br000025 article-title: Determining adsorption geometry, bonding, and translational pathways of a metal organic complex on an oxide surface: Co-salen on NiO(001) publication-title: J. Phys. Chem. C doi: 10.1021/jp311702j – volume: 90 start-page: 085421 issue: 8 year: 2014 ident: 10.1016/j.cpc.2015.05.013_br000175 article-title: Mechanism of high-resolution STM/AFM imaging with functionalized tips publication-title: Phys. Rev. B doi: 10.1103/PhysRevB.90.085421 – volume: 75 start-page: 949 year: 2003 ident: 10.1016/j.cpc.2015.05.013_br000010 article-title: Advances in atomic force microscopy publication-title: Rev. Modern Phys. doi: 10.1103/RevModPhys.75.949 – volume: 84 start-page: 1168 issue: 3 year: 1998 ident: 10.1016/j.cpc.2015.05.013_br000180 article-title: Resolution and contrast in Kelvin probe force microscopy publication-title: J. Appl. Phys. doi: 10.1063/1.368181 – volume: 66 start-page: 1 issue: 1 year: 2010 ident: 10.1016/j.cpc.2015.05.013_br000190 article-title: Kelvin probe force microscopy and its application publication-title: Surf. Sci. Rep. doi: 10.1016/j.surfrep.2010.10.001 – volume: 71 start-page: 125424 year: 2005 ident: 10.1016/j.cpc.2015.05.013_br000185 article-title: Accuracy and resolution limits of kelvin probe force microscopy publication-title: Phys. Rev. B doi: 10.1103/PhysRevB.71.125424 – volume: 325 start-page: 1110 issue: 5944 year: 2009 ident: 10.1016/j.cpc.2015.05.013_br000170 article-title: The chemical structure of a molecule resolved by atomic force microscopy publication-title: Science doi: 10.1126/science.1176210 – volume: 15 start-page: 141 year: 2001 ident: 10.1016/j.cpc.2015.05.013_br000080 article-title: A virtual non contact-atomic force microscope (NC-AFM): Simulation and comparison with analytical models publication-title: Eur. Phys. J. Appl. Phys. doi: 10.1051/epjap:2001175 – volume: 97 start-page: 044902 year: 2005 ident: 10.1016/j.cpc.2015.05.013_br000085 article-title: A virtual dynamic atomic force microscope for image calculations publication-title: J. Appl. Phys. doi: 10.1063/1.1841462 – volume: 22 start-page: 045702 year: 2011 ident: 10.1016/j.cpc.2015.05.013_br000200 article-title: The role of the tip in non-contact atomic force microscopy dissipation images of ionic surfaces publication-title: Nanotechnology doi: 10.1088/0957-4484/22/4/045702 – year: 2002 ident: 10.1016/j.cpc.2015.05.013_br000005 – volume: 1 start-page: 2196 issue: 9 year: 2014 ident: 10.1016/j.cpc.2015.05.013_br000125 article-title: Molecular design and control over the morphology of self-assembled films on ionic substrates publication-title: Adv. Mater. Interfaces doi: 10.1002/admi.201400414 – volume: 33 start-page: 385 issue: 4 year: 2002 ident: 10.1016/j.cpc.2015.05.013_br000035 article-title: Imaging and manipulation of biological structures with the afm publication-title: Micron doi: 10.1016/S0968-4328(01)00026-9 – volume: 25 start-page: 2850 issue: 5 year: 2009 ident: 10.1016/j.cpc.2015.05.013_br000155 article-title: True atomic-resolution imaging of (1014) Calcite in Aqueous solution by frequency modulation atomic force microscopy publication-title: Langmuir doi: 10.1021/la803448v – volume: 23 start-page: 325703 issue: 32 year: 2012 ident: 10.1016/j.cpc.2015.05.013_br000110 article-title: Non-contact atomic force microscopy study of hydroxyl groups on the spinel MgAl2O4(100) surface publication-title: Nanotechnology doi: 10.1088/0957-4484/23/32/325703 – volume: 18 start-page: 084017 issue: 8 year: 2007 ident: 10.1016/j.cpc.2015.05.013_br000105 article-title: Is atomic-scale dissipation in NC-AFM real? Investigation using virtual atomic force microscopy publication-title: Nanotechnology doi: 10.1088/0957-4484/18/8/084017 – volume: 72 start-page: S47 year: 2001 ident: 10.1016/j.cpc.2015.05.013_br000075 article-title: A mechanical approach to the dissipation process in NC-AFM: experiments, model and simulation publication-title: Appl. Phys. Mater. Sci. Process. doi: 10.1007/s003390100634 – volume: 80 issue: 6081 year: 1996 ident: 10.1016/j.cpc.2015.05.013_br000160 article-title: Parametric tip model and force distance relation for hamaker constant determination from atomic force microscopy publication-title: J. Appl. Phys. – volume: 47 start-page: 197 year: 2002 ident: 10.1016/j.cpc.2015.05.013_br000045 article-title: Dynamic atomic force microscopy methods publication-title: Surf. Sci. Rep. doi: 10.1016/S0167-5729(02)00077-8 – volume: 76 start-page: 637 issue: 1 year: 1982 ident: 10.1016/j.cpc.2015.05.013_br000130 article-title: A computer simulation method for the calculation of equilibrium constants for the formation of physical clusters of molecules: Application to small water clusters publication-title: J. Chem. Phys. doi: 10.1063/1.442716 – volume: 84 start-page: 115415 year: 2011 ident: 10.1016/j.cpc.2015.05.013_br000145 article-title: Atomic-scale dissipation processes in dynamic force spectroscopy publication-title: Phys. Rev. B doi: 10.1103/PhysRevB.84.115415 – volume: 84 start-page: 1801 year: 2004 ident: 10.1016/j.cpc.2015.05.013_br000070 article-title: Accurate formulas for interaction force and energy in frequency modulation force spectroscopy publication-title: Appl. Phys. Lett. doi: 10.1063/1.1667267 – volume: 57 start-page: 316 issue: 3 year: 1990 ident: 10.1016/j.cpc.2015.05.013_br000135 article-title: Improved atomic force microscope images using microcantilevers with sharp tips publication-title: Appl. Phys. Lett. doi: 10.1063/1.103677 – volume: 56 start-page: 2100 issue: 21 year: 1990 ident: 10.1016/j.cpc.2015.05.013_br000015 article-title: Optical-beam-deflection atomic force microscopy: The NaCl(001) surface publication-title: Appl. Phys. Lett. doi: 10.1063/1.102985 – volume: 23 start-page: 477 issue: 4 year: 2011 ident: 10.1016/j.cpc.2015.05.013_br000055 article-title: Recent trends in surface characterization and chemistry with high-resolution scanning force methods publication-title: Adv. Mater. doi: 10.1002/adma.201002270 – volume: 74 start-page: 235439 year: 2006 ident: 10.1016/j.cpc.2015.05.013_br000090 article-title: Noncontact atomic force microscopy simulator with phase-locked-loop controlled frequency detection and excitation publication-title: Phys. Rev. B doi: 10.1103/PhysRevB.74.235439 – volume: 76 start-page: 085414 year: 2007 ident: 10.1016/j.cpc.2015.05.013_br000100 article-title: Multiscale model of the manipulation of single atoms on insulating surfaces using an atomic force microscope tip publication-title: Phys. Rev. B doi: 10.1103/PhysRevB.76.085414 – volume: 23 start-page: 185306 year: 2012 ident: 10.1016/j.cpc.2015.05.013_br000140 article-title: Nanoscale periodic modulations on sodium chloride surface revealed by tuning fork atomic force microscopy publication-title: Nanotechnology doi: 10.1088/0957-4484/23/18/185306 – volume: 10 start-page: 2965 year: 2010 ident: 10.1016/j.cpc.2015.05.013_br000020 article-title: Unambiguous determination of the adsorption geometry of a metal–organic complex on a bulk insulator publication-title: Nano Lett. doi: 10.1021/nl101290t – volume: 31 start-page: 805 year: 1985 ident: 10.1016/j.cpc.2015.05.013_br000195 article-title: Theory of the scanning tunneling microscope publication-title: Phys. Rev. B doi: 10.1103/PhysRevB.31.805 – volume: 109 start-page: 146101 year: 2012 ident: 10.1016/j.cpc.2015.05.013_br000115 article-title: Measuring electric field induced subpicometer displacement of step edge ions publication-title: Phys. Rev. Lett. doi: 10.1103/PhysRevLett.109.146101 – volume: 75 start-page: 1287 issue: 4 year: 2003 ident: 10.1016/j.cpc.2015.05.013_br000050 article-title: Theories of scanning probe microscopes at the atomic scale publication-title: Rev. Modern Phys. doi: 10.1103/RevModPhys.75.1287 – volume: 59 start-page: 2436 issue: 3 year: 1999 ident: 10.1016/j.cpc.2015.05.013_br000065 article-title: Model of noncontact scanning force microscopy on ionic surfaces publication-title: Phys. Rev. B doi: 10.1103/PhysRevB.59.2436 – volume: 56 start-page: 16010 year: 1997 ident: 10.1016/j.cpc.2015.05.013_br000060 article-title: Forces and frequency shifts in atomic-resolution dynamic-force microscopy publication-title: Phys. Rev. B doi: 10.1103/PhysRevB.56.16010 – volume: 76 start-page: 245421 issue: 24 year: 2007 ident: 10.1016/j.cpc.2015.05.013_br000095 article-title: Dynamical processes at oxide surfaces studied with the virtual atomic force microscope publication-title: Phys. Rev. B doi: 10.1103/PhysRevB.76.245421 – volume: 9 start-page: 600 year: 2013 ident: 10.1016/j.cpc.2015.05.013_br000150 article-title: Free energy approaches for modeling atomic force microscopy in liquids publication-title: J. Chem. Theory Comput. doi: 10.1021/ct3008342 – volume: 26 start-page: 261 issue: 8 year: 1996 ident: 10.1016/j.cpc.2015.05.013_br000030 article-title: STM and AFM of bio/organic molecules and structures publication-title: Surf. Sci. Rep. doi: 10.1016/S0167-5729(97)80003-9 – volume: 107 start-page: 036102 year: 2011 ident: 10.1016/j.cpc.2015.05.013_br000120 article-title: Stable cation inversion at the MgAl2O4(100) surface publication-title: Phys. Rev. Lett. doi: 10.1103/PhysRevLett.107.036102 |
| SSID | ssj0007793 |
| Score | 2.2077904 |
| Snippet | Non-contact Atomic Force Microscopy (NC-AFM) is an experimental technique capable of imaging almost any surface with atomic resolution, in a wide variety of... |
| SourceID | proquest crossref elsevier |
| SourceType | Aggregation Database Enrichment Source Index Database Publisher |
| StartPage | 429 |
| SubjectTerms | Atomic force microscopes Atomic force microscopy Computer simulation Mathematical models Modular NC-AFM Programming languages Python Simulation SPM Stress concentration Summaries |
| Title | Flexible and modular virtual scanning probe microscope |
| URI | https://dx.doi.org/10.1016/j.cpc.2015.05.013 https://www.proquest.com/docview/1778025871 |
| Volume | 196 |
| WOSCitedRecordID | wos000362602900040&url=https%3A%2F%2Fcvtisr.summon.serialssolutions.com%2F%23%21%2Fsearch%3Fho%3Df%26include.ft.matches%3Dt%26l%3Dnull%26q%3D |
| hasFullText | 1 |
| inHoldings | 1 |
| isFullTextHit | |
| isPrint | |
| journalDatabaseRights | – providerCode: PRVESC databaseName: Elsevier SD Freedom Collection Journals 2021 customDbUrl: eissn: 1879-2944 dateEnd: 99991231 omitProxy: false ssIdentifier: ssj0007793 issn: 0010-4655 databaseCode: AIEXJ dateStart: 19950101 isFulltext: true titleUrlDefault: https://www.sciencedirect.com providerName: Elsevier |
| link | http://cvtisr.summon.serialssolutions.com/2.0.0/link/0/eLvHCXMwtV1La9tAEF7apIVeQp8kTVtUKD00qGgf0q6OIdi0JTg5OODbIq0lUHAk1XJCfn5ndleSm9KQHgpGGLGSzc6nmU_zJOQTA6sflxLjg4KHIlE2CQCeK2mKmCbMsELYYRNyNlOLRXruSwg6O05A1rW6vU3b_ypqOAfCxtLZfxD3cFM4Ad9B6HAEscPxQYKfYotLrIdCl_hVs7R5pjfV2haKdMbNKMK8rLw4usJ0PFuYsk1S-0kP3u3RYd75WEUykHAwc8Y5vLfzeafYnaIy1dFJhvNWLTlGn03bjLq96rLaqbuz1aoaUoCyZsiy9wET746gsa_L21KxoNixKdtvKjbdVpLC-zicvRWuu8sfqtx5FS6_mhY7TdLYNVjlo93qY_WzMz29OD3V88li_rn9GeJEMYy8-_Eqj8kuk3EKSnv3-Ptk8WOw01L6lsz-D_cxb5v9d-dX_8Za7thvS0rmz8mef5sIjh0KXpBHRf2SPD13YntFkh4LAWAh8FgIPBaCHguBxUIwYuE1uZhO5iffQj8oIzSggjeh5LzME85KSjORx6osSrM0KoqzqExZKUSOc1gNVUsWpUyyPFKpKBnnRVYYFnH-huzUTV3skyBNVEZzhcTbYGchBWtSeKcE0gLcOEsOSNRvhDa-izwOM1npPl3wUsPeadw7HcGH8gPyZbikdS1U7lss-t3VngM6bqcBF_dd9rGXhAb9iEEvAHJz3WkqpQJeryR9-4A1h-TZCOp3ZGezvi7ekyfmZlN16w8eQb8AS_WFHg |
| linkProvider | Elsevier |
| openUrl | ctx_ver=Z39.88-2004&ctx_enc=info%3Aofi%2Fenc%3AUTF-8&rfr_id=info%3Asid%2Fsummon.serialssolutions.com&rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&rft.genre=article&rft.atitle=Flexible+and+modular+virtual+scanning+probe+microscope&rft.jtitle=Computer+physics+communications&rft.au=Tracey%2C+John&rft.au=Federici+Canova%2C+Filippo&rft.au=Keisanen%2C+Olli&rft.au=Gao%2C+David+Z&rft.date=2015-11-01&rft.issn=0010-4655&rft.volume=196&rft.spage=429&rft.epage=438&rft_id=info:doi/10.1016%2Fj.cpc.2015.05.013&rft.externalDBID=NO_FULL_TEXT |
| thumbnail_l | http://covers-cdn.summon.serialssolutions.com/index.aspx?isbn=/lc.gif&issn=0010-4655&client=summon |
| thumbnail_m | http://covers-cdn.summon.serialssolutions.com/index.aspx?isbn=/mc.gif&issn=0010-4655&client=summon |
| thumbnail_s | http://covers-cdn.summon.serialssolutions.com/index.aspx?isbn=/sc.gif&issn=0010-4655&client=summon |